Rom Hacks

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As a general rule, most ROMhacks you'll see on Pokécommunity are shitty. However, a lot of great ROMhacks can be found if you just keep looking.
If you think there is a hack that should be added to this list, just say it in the thread, I'll see if I can put it in here.

>How to patch a ROM
It's not rocket science.  Most are in IPS format, so things you need for this:
-The Patch
-The ROM it requires (read up, as sometimes they want a specific version)
-A copy of LunarIPS, MultiPatch if you're a macfag.

1. Get LIPS or MP ready to go.
2. Click on it and direct it to the ROM and patch, in the case of LIPS you can even click on the patch itself to make things easier.
3. Play it.  If something screws up consult the hacker's directions.  If you have the correct ROM and all try again.

>151/251/286/493/649 and difficulty hacks
This term came to being out of a simple hacking process in ROMs that everyone likes: Make all Pokemon catchable, and make the difficulty a little harder (the best ones being CONTRA HARD if done in a Nuzlocke).  Along with a few other modifications such as starters being altered and giving you the National Dex early in the game if needed.  Examples are:

Gen 1:
Red Proud Eyes Version: Difficulty hack, adds Gen II graphics, changes movesets, general stuff.
http://www.pokecommunity.com/showthread.php?t=279077

Gen 2:
Pokémon Crystal Emu Edition: Simple 251 hack.
http://www.romhacking.net/hacks/1420/

Pokémon Pure Silver: An interesting take on the 251 hack, rare Pokémon and Legendaries being placed in their own added sidequests. Webpage has been taken down, but the archive has a working DL link.
https://web.archive.org/web/20120822114724/http://web.mit.edu/skishore/www/pokemon251.html

Pokémon Crystal Enhanced: Difficulty hack, adds all 251 Pokémon.
http://s7.zetaboards.com/Nuzlocke_Forum/topic/8544349/1/
https://www.sendspace.com/file/t68dfh

Pokémon Crystal Kaizo: Similar to the above, but taken up to masochistic levels. Prepare your anus.
http://www.pokecommunity.com/showthread.php?t=334713

Gen 3:
Pokémon UltraViolet: A simple 386 hack of FireRed, adding new Pokémon in logical locations.
http://www.romhacking.net/hacks/1156/

Fire Red Omega: Makes all Pokémon obtainable, changes the starter, ramps up the difficulty. Not much else to say. It'll have you thinking quite a bit more about strategy than most mainline Pokémon games
http://www.mediafire.com/?evxxa2wa7drkzpn

Yet Another Fire Red Hack: Really it's exactly what it claims to be. However, it adds in the physical/special split, new pokemon from other generations, removes trade evolutions from the game, making most of them simply level up evolution. Starters have changed, most gym leaders use new types due to the new pokemon they have at their disposal.
http://www.pokecommunity.com/showthread.php?t=289571

Emerald Complete National Dex Edition: A standard 386 hack focusing on adding all 386 Pokémon and then mixing up trainer teams to accomodate the increase in Pokémon
http://www.romhacking.net/hacks/1991/

Eccentric Emerald: Another 386 hack with slightly increased difficulty, also has the physical/special split of the newer games.
http://www.pokecommunity.com/showthread.php?t=301368

Gen 4:
Bloody Platinum: Just another difficulty hack, with some new things put in. Starters are difficulty, Elite 4 are damn near impossible to beat. Male and female pokemon have different sprites now, a lot of overworld sprites are changed. Some routes hold up to 14 different Pokémon.
http://gbatemp.net/threads/%C2%B8-%E2%80%A2-%C2%A8pokemon-bloody-platinum%C2%A8-%E2%80%A2-%C2%B8.167328/

Platinum Enhanced: Same deal. All Pokémon available, your starter is a dragon type and you get it in an unconventional way. Gyms all have six Pokémon, movesets are buffed, and Pokémon normally found in honey trees are now in the wild. No more slathering for hours just to get that Combee.
http://www.mediafire.com/?f3c3i62okjn9qds

Flawless Platinum: A newer 493/difficulty ROMhack, gym leaders have full teams and most trainers have relatively strong pokemon. It also has revamped/buffed Pokémon, moves and movesets.
http://www.mediafire.com/download/4z4hbyu1p99u7i6

Sacred Gold and Storm Silver: HG/SS hack by Drayano. There's an increased difficulty curve, great pokemon availability, and changed evolutions. HMs are powered up, and Pokémon are given new moves to use whilst leveling up.
http://gbatemp.net/threads/pok%C3%A9mon-sacred-gold-storm-silver.327567/

Mind Crystal: HG/SS hack by MeroMero originally in French.
Fairy types and difficult trainers.
Info:
https://projectpokemon.org/forums/showthread.php?48029-Pok%C3%A9mon-MindCrystal
DL converted to English:
https://mega.nz/#!SwNF2LwJ!9RuiKJ3DhkQ_fxDG9s1sxr_NjslRAfyP6yi0CNQiu1w


Gen 5:
Blaze Black / Volt White: Drayano hack; changes stats, types, moves, abilities, difficulty and such. If you've played some of the other games he's made you know what to expect. There's nothing really new to the story here. it's just minor tweaks.
http://gbatemp.net/threads/pok%C3%A9mon-blaze-black-pok%C3%A9mon-volt-white.286850/

Blaze Black 2 / Volt White 2: A successor to Blaze Black / Volt White, Similar to the original except that its based on Black 2 and White 2.
http://projectpokemon.org/forums/showthread.php?26326-Pok%E9mon-Blaze-Black-2-amp-Pok%E9mon-Volt-White-2

>More advanced hacks
Gen 1:
Pokémon Brown: Awesome RBY hack with a few GSC Pokemon in, and a completely new region with even some parts inspired by RBY betas.  Don't play this on real hardware and turn off the VRAM in BGB, hacker fucked up the memory a little making the sprites garbage if played that way.
http://www.rijon.com/brown/

Pokémon Maize: Promising hack, currently a four-Gym beta. A lot of updated mechanics, interesting NPCs and small sidequests, and well-made custom music. Has a built-in Nuzlocke option that enforces the rules.
http://www.pokecommunity.com/showthread.php?t=309293

Pokémon Red Battle Factory: A fun little hack that serves to recreate the Battle Factory from Emerald in Gen I. Surprisingly addicting.
http://www.romhacking.net/hacks/1966/

Gen 2:
Pokémon Prism: The sequel to Brown. Set foot the entirely new region of Naljo, and travel back to Rijon. Currently in a four Gym beta, though the development for the game has been speeding up (only took seven years). Features some of the best ASM to ever grace a Pokémon hack.
http://www.rijon.com/prism/

Pokémon Dark future: Pretty normal hack until someone fucking comes from the future and tells you that Team rocket are finding a very strong leader who is capable of taking over the entire planet. To change this dark future, you'll embark on an adventure with your Eevee starter, and even train under lance himself.
http://www.pokecommunity.com/showthread.php?t=205244

Pokémon Dark Energy: A really different hack than most. While the gameplay is Pokémon, the game is inspired by and structured like more traditional JRPGs like Final Fantasy and Chrono Trigger. Features a monstrous amount of content for a beta and includes a metric ton of optional side content. Fairly plot heavy.
http://www.pokecommunity.com/showthread.php?t=266372

Pokémon Bronze: Try to look past the spritework. A very vanilla hack set in the fan region of Kohto. Follows the traditional Pokémon game structure but at the same time stands as its own region. Good for someone looking for a fresh Pokémon experience without risking any freaky fanfiction bullshit.
http://www.pokecommunity.com/showthread.php?t=280588

Touhoumon Ordinary Version: Emerald version (listed below) is generally recommended for people wanting to get into Touhoumon, but for someone familiar with the concept, this is a neat Gen II hack with the proper Touhoumon flair. Follows the plot of GSC swapping out names and editing locations to make sense with Touhoumon.
http://hax.iimarck.us/topic/1485/

Gen 3:
Pokémon Flora Sky: A game that gets very polarized opinions. While some people despise it, others revere it. Set in a new region, pokemon from 4th and 5th gen are available to capture and train. Shaymin is the main legendary of this game, though you meet many of the others along the way. The story of a fight between Palkia and the portal that they open, unleashing Giratina.
Has some serious backtracking and sometimes leaves you with no idea where to go. Make sure to have a walkthrough handy.
http://www.pokecommunity.com/showthread.php?t=183562

Pokémmo: An MMO version of Fire Red.
pokemmo.eu

Pokémon Dark Violet: A FireRed hack that at first glance appears to be a difficulty hack, but it adds in a completely new plot and completely rearranges the region. Features great custom graphics and music.
http://www.pokecommunity.com/showthread.php?t=291789

Azure Horizons: A really well polished, enjoyable FireRed hack set in a new region with a good story, great mapping and great scripting
http://www.pokecommunity.com/showthread.php?t=151068

Pokémon Vega: another very well polished FireRed hack set in a new region with loads of fakemon. It is sometimes very difficult and the language barrier doesn't help, but it is a fan favourite of many.
http://www.2shared.com/file/hOSk1dY8/Pokemon_-_Vega_J_.html

Sienna: another polished, 8-gym hack following the plots of two Team Rocket factions in the new Voultan region. It stars some well-sprited fakemon and has great mapping and scripting.
http://www.pokecommunity.com/showthread.php?t=202372

Touhoumon Emerald 1.812: Want to go into Touhoumon, the hacks that replace all Pokemon with Touhou?  First play this!  It has far better balance along with far less bullshit compared to most other Touhou hacks, and it even has a fully functional Battle Frontier.  Made to challenge by movesets alone, so bring your brain.  This also means it's worth trying out if you love hacks like Yet Another Fire Red Hack.
http://www.pokemonhackersonline.com/showthread.php?t=13278-Touhou-Puppet-Play-1-812-Emerald
Type chart for v1.8 hacks, you WILL need this: http://thpp.supersanctuary.net/wiki/Type_Chart

Snakewood: Don't come into this hack serious. It's rather polarizing, but some find the hack to be a great parody of poorly-done ROMhacks. Expect overpowered Fakemon, an extremely over-the-top zombie plot, and plenty of gainax.
http://www.pokecommunity.com/showthread.php?t=235371

Liquid Crystal: A Johto remake. Features day/night, random weather, Gen V's exp system, and various other goodies. Be warned, the plot takes a pretty hard beating, so avoid if you demand faithfulness to the originals.
http://www.pokecommunity.com/showthread.php?t=242023

Crystal Dust: Another Johto remake. More faithful to the games than Liquid Crystal, though not as far into development. It's been getting more love as of late, and occasionally the devs bring updates to /rhg/. Considered the superior game to Liquid Crystal, just in need of more love.
http://www.pokecommunity.com/showthread.php?t=234566

>Universal Pokemon Game Randomizer
This solves all your randomizing questions in one fell swoop: able to randomize any main Pokemon game in current existence with more options, and you can even create the same random game more than once for racelockes and competitions.
http://pokehacks.dabomstew.com/randomizer/