The Addons
Unless noted, all the addons are hosted on Curse.com.

There are a few things that have been baked in to default now. I will try to note what I can that has replaced an existing addon.

The addons listed here should all be working with 6.0/WoD. As of 11-15-14, addons marked with an * have not been/may not be updated.

Total UI Replacements
TukUI – A Base setup that strips default down to a bare-minimum look. You will probably have to install some additional addons to get some more features.

ElvUI – Basically it is TukUI with a lot of things baked in as part of its default. Everything is configurable.

Both are available on the same page. They have their own client to keep them updated if you wish.

Since both Elv and Tuk have their own active forums it may be best to browse there for any questions, though there are a few people here that use it and could help.

RealUI – WoWInterface - A quirky replacement using radial and custom bars. Give it a go if you want something different


Addon Management
+ - Addon Control Panel - In-game addon control. You can create addon sets that you can load as you need. + - A lot of this is part of default now with the exception of sets.

Reflux – Allows you to make addon profiles on your characters. Might not be as needed as you can turn addons on and off in the game now.


Bar Mods
Bartender4 - Lets you have access to all 120 buttons (mostly) at once. Some basic layout options

Dominos - Same as above really.

OPie - You could use this as a bar replacement. I think it is really intended to make pretty circle bars for not-often used stuff.

* - Ion – This is on Curse as well but not updated currently there. A massively customizable bar addon. It does not link to default (if you switch computers). * - It has been picked up by a fan and does work for 6.0 mostly (link in the comments). Unknown if the original author is coming back.


Unit Frames
PitBull Unit Frames 4.0 – Very customizable, but has a somewhat steep and unintuitive setup.

Perl Classic Unit Frames – A fairly simple re-skin of default.

X-Perl Unit Frames – Perl with more stuff.

Stuf Unit Frames – A basic reskin of the default unit frames with self described limited options.

Shadowed Unit Frames – Extremely customizable with an easy learning curve.


Raid Frames
The default Blizzard UI includes raid frames that can also be used in 5-man parties. They have a similar look to Grid. Also most of the Unit Frame addons have Raid Frames as part of their setup.

HealBot Continued – Everything you need to whack-a-mole heal. The setup can be a bit daunting.

*Grid – Simple raid/party frames for use with healing. It uses additional addons, called Modules to add in more functionality. * - It may, I haven't tested it personally.

Grid2 - Very similar to Grid but it comes with a number of the modules as part of the addon itself.

VuhDo – An all-in-one healing and frame addon. Allows you to click to cast on party members. Setup is somewhat intuitive but can take a bit of time.

Clique – A mouseover Click to Cast addon. If you use Grid, Grid2, or the default frames you cannot click to cast by just mousing over your target unless you use macros for each spell. This mod allows you to do that for every frame in the game (remember to turn off frames you don’t want click to cast turned on for) using a new tab on your spellbook.


Casting Bar
Quartz – Full casting bar replacement. Lets you see all the casting bars, place them where you want.

Gnosis - Castbar and timer addon. Can also do buffs, debuffs and cooldowns.


Raid/Boss Notification
BigWigs Bossmods – Gives you easy to see notifications of bosses' abilities in movable notification areas. Additional Modules for older content and LittleWigs for 5-mans.

*Deadly Boss Mods – Same as BigWigs but also does 5-man bosses by default. It is a personal preference on which you like more. Also does past expansions as Modules. * - Reported to have issues with Quest Items.


Notifications
WeakAuras 2 - THE addon to let you know about anything in the game. It can function as many things, but the learning curve can be something else. Uses a script setup. You can find scripts around with some googling if you don't want to figure it out yourself. Seriously, it is that powerful and good.

Power Auras Classic – WoW has a basic version of this as default now. With this you can completely customize how you get notifications for pretty much anything in the game.

TellMeWhen - Similar to WA2. Can track many things and let you know when they are ready/down/up and so on. The mod page has usage examples you can directly import in-game.

GTFO - Screams at you if you are standing in something you shouldn't be.

Hear Kitty - Audio notifier for combat resources, such as combo points or Holy Power.

ExtraCD - Graphically shows you the internal cooldowns on talents, skills and gear. Lets you monitor PPM.

NugRunning - Customizable timers for every ability. Multi-target. Also supports cooldowns, spell activation overlay, totems, drain soul ticks, aoe timers, internal cooldowns.

IceHUD - The original HUD setup. It has had a lot added to it over the years, all of it can be turned on or off. A lot/all of it's functionality can be replaced by WA2, however the setup of this is much simpler.

BadPet - Lets those with pets know when Growl is on. By default it whispers it to the owner, can also announce it in chat.


Minimap
SexyMap – A minimap with many options for different looks to fit almost any theme. Allows you to move the quest and durability frame, and other options.

Chinchilla Minimap – Not quite as many flashy looks as SexyMap, but a solid and option filled addon.

SquareMap - It's a square mini-map. You can move it.


Questing
The default Blizzard UI is pretty robust and includes quest tracking and map blobs to show the location of quest objectives and turn-ins on the map. I believe every quest addon just ties into default now.

*All of these besides Work Complete may be a while till they get updated. For existing quests they should still function, WoD use is still unknown.

QuestHelperLite – Does quest pathing and ant trails, it uses the game's own database.

Lightheaded - WoWInterface – Expanded Quest frame and imports comments from WowHead to the in-game quest frame.

TomTom – An arrow mod that will point you in the direction of your quest/objective. Advised to use with Lightheaded.

Carbonite – An all in one quest tracking mod. Has its own Google Maps style minimap (can replace the world map too) with many options. I recommend that you turn off a number of them (especially the spammy stuff). It also has the orc from below. - Fan Update has it mostly working. Official update still being worked on.

Work_Complete - The orc peon we all know and love chimes in when you complete quest objectives. Alliance fanatics, you're out of luck.


Chat
Chatter – A very customizable chat mod. Many options for text, font, links, channel names, colors.

Prat 3.0 – Also a customizable chat mod that is broke down to modules to handle all the options.

PhanxChat - Similar to the others. Personal preference more than likely.

Cellular – IM mod that allows you to change the appearance of in-game whispers.

WIM (WoW Instant Messenger) v3 - Lets you create an IM feel to Whispers. Separate or tabbed windows for whispers. Customization and history options.

Misspelled – In-game spell check with auto-suggest.


Rare Finder

*Functionally these don't work the way they did and may not for a while.

SilverDragon – Scans for rare mobs and alerts you when they are near. Limitation is that you have to click on the mob or have nameplates on.

_NPCScan – Essentially the same as SilverDragon with a bit more flash to notify you of a rare. You can also get _NPCScan.Overlay which lays a colored swatch on the maps showing where the rares spawn and wander.

RareFinder - Adds skulls to your Map showing the location of every known rare in Draenor. It notes if you have killed them or not. A really handy addon.


Achievements
Overachiever – A replacement for the Achievement window that allows searches plus gives help for some achievements.

AchieveIt - An enhancement for the default Achievement window. Breaks down the different achievements into categories and locations.


Bags/Storage
Note - Storage has gone through a pretty significant update with 6.0/WoD. Sorting, trashing, custom bag designation are now part of default. See if the default setup suites your needs. Some might work but might not have the default features worked in yet.

ArkInventory – Not just a one-bag, but also a sorting mod with many options organizing your stuff.

AdiBags - Light-weight one-bag mod, with auto sorting and filtering.

Scrap – Automatic junk-seller. Has plugins to hook into bag mods such as Bagnon and Combuctor.

Bagnon – An all-in-one bag mod with sorting options.

Combuctor - An all-in-one bag mod with auto sorting and filtering. Has a ton of plugins.

Baud Bag - An individual or all-in-one bag setup. Some skinning and search options, but also lets you move your bag/bags.


Gear
The default Blizzard UI includes a multi-set setup, with name and picture. Pretty easy to use and get going.

InspectEquip – Adds on a second panel to all character screens, showing average iLevel, name and location gear comes from, and if it is enchanted.

Examiner – An enhanced Inspect frame that stores those you inspect as well as shows more details on stats, gear, professions, gems, and talents.

ItemRack - A mod to make swapping equipment easier through popout slot menus, equip slot buttons, gear sets and automated swaps.

Moncai Compare - Lets you automatically show the compare window when you mouse-over any piece of gear.

Simple iLevel - Shows you the ilvl of a character in the tooltip. Has some extra options as Modules if you want more/to show more info.

Outfitter - The author may be back for WoD.


Mounts & Pets
One button, favorites, random is part of default. The button is in the top left corner of the Mount and Pet window.

GupPet – More options than default it looks like.

Yay Mounts - This works with Druid and Shaman forms (default doesn't as far as I know) as well as vehicles.

Bunny Hunter - Lets you know how many times you have looted that mob and not had it drop its damn pet.


Pet Battles
BattlePetCount - Shows whether you already own a battle pet via tooltip, pet battle or creature cage and what level it may be.

Pokemon Trainer - Adds information to Wild Pet tooltips, and shows information about your enemies' abilities and vulnerabilities during battle.

PetJournal Enhanced - Lots of additions to the pet journal. Sorting, filter by zone, pet specialization, etc.

Pet Battle Quality Glow - WoWInterface - Shows quality and rarity of battle pets by adding a glow border and name color.

PetBattle Teams - Save 60 pet battle teams for use later. It's like Outfitter for pets.

Battle Pet Tabs - Similar to the above mod, 8 teams with tab interface. Authors Note - Delete the BattlePetTabs.lua from your WTF folder before loading in 6.0

Pet Battle Pokemon Mod - Get the authentic pet battling experience with Pokemon music!


Tooltip
TipTac – Allows you to change the layout, placement, and behavior of your tooltip. Yup it's the only one listed. It is that good.


Map
Mapster – Allows re-sizing, alpha, coordinates, and fog of war changes of the World Map.

Cromulent – Zone levels, fishing skill, and dungeons in a zone. Works with default and Mapster.


Taxi
Flight Map and Time – Shows cost and flight time.

Flight Map Enhanced - Gives you a timer, as well as sortable lists of where flight points are and where you go.


Name Plates
Tidy Plates – A re-skin of the nameplates above a mob's head. Allows a variety of customization in itself and though some additional Modules.

Tidy Plates: Threat Plates – A Module to Tidy Plates that shows the threat on mobs to you in the nameplates. A great addon for new and experienced tanks, as well as DPS and healers who want to know which of those dozen trash mobs are gunning for them.


Cooldown Management
Some of the addons listed under the Notifications section can accomplish this.

OmniCC – Shows you a nice clean number counting the cooldown of an item and spells on your bar and in your bag. Also can do a pulse of the item/spell on your toolbar when it is ready to be used. A form is in as Default, probably want to stick with this though.

CoolLine Cooldowns – Shows your spell cooldowns on a bar with easy to see time segments.

ForteXorist – Shows the cooldown on your spells/abilities on a per bar basis.

NeedToKnow - Customizable cooldown bars. Can also be used to track buffs and debuffs.

AdiButtonAuras - Replacement/update to Inline Aura. Combines target plus your own cooldown and places it on the button in your bar.


Buff/Debuffs
Elkano’s BuffBars – On the surface it is a simple buff/debuff display. Shows bars with name, time, and icon for all buffs and debuffs. Can be completely customized, but the learning curve can be seen as a bit annoying.

Raven - Not only does it do buffs and debuffs but it is also a spell timer. Comes pre-configed but can be customized.

ClassTimer – Shows buffs and debuffs that just you do in a bar format. Adjusts to each class automatically. All bars can be moved.

Decursive - Yes it is still around. Cleansing mod for easy removal of poisons and the like.


Combat Text
Default – A very basic setup of combat text is in the game. Use these if you want more control.

MikScrollingBattleText – Puts damage out and in, heals out and in, as well as notification (ability procs, cooldown timers, combat notification) in its own frames, all of which are customizable and movable.

Parrot - Floating text mod made by ckknight (he's wrote a lot of addons). Customization is on par with Miks.

xCT+ - A third option for combat text and notifications. Author is working on an update.


Combat Logs
Skada Damage Meter – A modular combat log that can show a number of different summaries from fights. Almost all the options are also separate Modules. Many layout options, and can function as a threat meter.

Recount – A damage meter. Can show breakdowns, can auto/be reset. It's good if you need the basics but want to dig a bit deeper as well.

Details! - The new meter to come out. It is still early in development so use if you want. Similar to Skada in that it can be modular and broke apart to different windows. It is pretty and can get in-depth as well.


Threat Meter
Default – A basic threat meter is in WoW. Shows as a small percentage bar over the mob's portrait. Use these for more options.

Omen Threat Meter - Shows threat in a window. Can do warnings and the window is very customizable.

Skada and Details – See link above – Both can also function as a threat meter.


Crafting
Skillet – Complete redo of the crafting frame. Allows queuing of items, semi-automatic sub crafting, tracks inventory on multiple character, custom sorting, skill point coloring, many options.

Panda - Handy add-on for speeding up repetitive tasks such as prospecting and milling.

Molinari & xanMortalPestle - Similar to Panda, hold Alt and click to prospect, mill, etc.

TradeSkillDW - Makes the default tradeskill window double pane and adds in tabs to easily swap to your other professions.

Ackis Recipe List - Database of every recipe in the game and where to get them (if you still can on a few). It uses Modules now for each profession, listed on the addon page or you can get them through the Curse Client.


Gathering
GatherMate2 – Shows icons for herbs and ore on your mini-map and the world map. Learns as you go or you can import data from GatherMate2 Data.

Gatherer - Similar to GatherMate2. It has GathererDBWoWHead as its data source.

Archy - Great archaelogy helper, even integrates with TomTom, double right-click casting in dig zones without a button, simple UI that has two options (normal or minimal) and can be setup to automatically add your keystones.

Fishing Buddy - A fishing addon that keeps track of the fish you catch and helps manage your fishing gear.


Looting
XLoot 1.0 - Options for showing loot windows in a different manner. Some additional features are available through additional Modules.

AtlasLoot Enhanced - Lets you know what every raid, dungeon, and world event boss drops. Also what you can buy from the gone Valor and Justice Points. Has Crafting and reputations as well, all easily searchable or done through drop-down menus and buttons. * - Updated for 6.0, some older stuff is missing. Give it time.


Auctions
There have been some basic changes in default, but to make money look at these.
Auctioneer - Self Hosted – The old boy. Comes as either a complete package with 18 individual addons (with a lot of interdependency) or as separate downloads. Known to use a lot of your CPU and memory. Honestly it might be time to move on.

Auctionator – Easy buying and selling of items at the AH in a redone Auction House interface.

TradeSkillMaster - Despite the name, this mod covers auctioning as well as professions. It is a LOT to take in trying to get this going. There are YouTube vids to help with the setup, as well as a desktop application that updates your prices. The Gold-Making Thread is going to be a better place to ask about this one than here (or google maybe).

Mobile Armory - Blizzards own App lets you buy and sell stuff on the AH. It's a pretty robust app and can be nice if you go out in the actual world once in a while.


Mailbox
Postal – Adds multiple features to the mailbox. Useful for auto-opening from certain sources.


Looks
Masque – Formerly known as ButtonFacade. Allows you to re-skin buttons. Multiple skins are available here.

Sunn's Viewport Art – Want to see less of the game world (rendered portion of the game screen)? This lets you re-size what you can see. Useful for customizing, especially if you like pretty pictures. Many Art Packs are available. It is however very valuable if you plan to play on multiple monitors.

Skinner – Re-skin (almost) every default panel in the game as well as many addon windows. Lets you do alpha as well as colors and art. May be a bit wonky with some of the new windows for a bit.

MoveAnything - Move, scale, hide just about any default frame in the game. NOTE - This may or may not get updated for WoD. A fan update for MoP is here.

GnomishVendorShrinker - Compacts vendor frames to show one item per line, among other features.

Kong Automatic UI Hider - Allows fading of any UI element that already doesn't have fading in its configuration. Examples including mouse-over, in combat, instance type.


DataBrokers/Display
ChocolateBar Broker Display – Puts a bar at the top of your screen (default location) to display many things, and multiple addons tie-in to it to display stuff for them, sometimes with separate Modules sometimes not.

Titan Panel - The original display bar. Offers a bunch of modules that tie into it and can display data from other mods.

MinimapButtonBag - Takes all those buttons on your minimap and puts them in a single button that expands to a bar/bars.

Bazooka - Bar at the top, other addons hook into it, flavor choice between Chocolate, Titan, or this.


Miscellaneous
CoolLevelUp – More flash and some more detail when you level. For those that don’t like the default notification.

Altoholic - Lets you know everything about your alts without having to switch to them (you do have to log in once and open everything so it can cache it all). Also adds data to item tool-tips so you can see which of your characters is carrying what where (bags/bank/AH), though this requires DataStore (made by the same author) and is installed with Altoholic. If you run alts, you want this addon. - Unknown if this is working for Garrisons.

BadBoy - Blocks and reports gold spam, hacking spam, SusanExpress. Helps clean up your chat window.

AskMrRobot - Should still help for gems and enchants. Might be worth holding on to for a bit.

Gnomish Interrupter - Announces when you miss or connect with an interrupt.

GlyphStatus - Hesitant to list this one as I've been getting some errors lately. Turn it off when you aren't going to use it. Open up your Glyph pane it notes what glyphs you don't have. If you then have a Scribe you can open up the list for that character and see what they need, otherwise keep the list open for a shopping list.


Hunter
Improved Stable Frame - An expanded and somewhat customizable stable frame for Hunter pets.


Mage
Mage Candy - Lots of options to let you mage better like monitors, timers, trackers. If you mage it can be handy.


Monk
*Storm, Earth, and Fire - An almost required addon for monitoring your clones as a WW monk. - Check the comments for a fix that makes it work. Requires a little lua editing.

Garrisons

Broker Garrison - A broker addon for the addons that handle them (TitanBar, Bazooka, ChocolateBar) showing your garrison missions reportedly across all characters.

Garrison Mission Manager - This adds three buttons to the side of the mission window that will auto-assign the followers with the best abilities to a mission. Shows the top 3 options with any time and/or XP bonuses.

MasterPlan - On the surface, it makes finishing all missions a 3-click event. It also breaks down your followers showing how many of what you have, plus it shows the rewards and cribbed a bit from GMM showing the top odds of finishing a mission. Updated almost daily as they add/tweak more things.

If you think you can do better, well you can give it a shot. All addons are coded using lua and XML. There is even a book you can get to help you get started. If you run into some serious issues find the addon page and post about it (with a copy of the error for bonus points).