WARNING: Town mods may lower your frames, this is the down side to town mods. Using these mods will more than likely cause a drop in frames.
Town and City mod guide
First off the big mod:
JKs Towns and Cities overhauls - http://www.nexusmods.com/skyrim/users/1305814/?tb=mods&pUp=1
These are amazing overhauls that add more clutter to the major cities in Skyrim. As well he did the small towns that add more clutter and some buildings. These mods are more hard on FPS but if you have frames to spare id suggest it.
Mods that add more to the already existing towns of Skyrim:
Enhanced Solitude: https://www.nexusmods.com/skyrim/mods/93424
The best Solitude mods, merged together into a single plugin, with multiple fixes, tweaks and enhancements.
SKY CITY Markarth Rising - http://www.nexusmods.com/skyrim/mods/58366/?
A slight overhaul mod that adds new buildings and NPCs to the mountain-side that Markarth is located in. This makes the mod 100% compatible with JK and Dawn of Markarth. These new buildings and structures are connected via dwemer lifts built into the mountains. Most of the new buildings can be entered and you will find new shops high in the sky of Markarth. It also has an exterior option that add unenterable buildings outside of Markarth. I personally use it just to add clutter outside the town.
Windhelm Exterior Altered - Windhelm Exterior Altered Optional - http://www.nexusmods.com/skyrim/mods/50977/?
Adds a small dock on the opposite side of the Windhelm bridge. Helps make Windhelm seem more important.
Windhelm Bridge Overhaul - http://www.nexusmods.com/skyrim/mods/50243/?
This small mod edited the bridge to Windhelm to feel more important. It adds more guards and guard barracks and even adds a few stalls to the bridge to help it feel lived in. Recommended to get the version WITHOUT the giant upscaled tents.
Whiterun Expansion Redone - http://www.nexusmods.com/skyrim/mods/80269/?
A massive mod that adds to the side of Whiterun, right next to the farms added by CRF. This mod adds new npcs, shops and inns as well as connecting itself to the main city. This mod is highly recommended too add a slums like area outside Whiterun. Something to show that the walls of the city have collapsed over time.
Shezrie's Old Hroldan Town - http://www.nexusmods.com/skyrim/mods/71875/?
This mod adds a town around the Old Hroldan Inn. The town has custom voices and even quests. The town itself is very cluttered and close and gives that major city feeling.
Expanded Winterhold Destruction Ruins - http://www.nexusmods.com/skyrim/mods/30554/?
Adds the ruins of the Great Collapse around Winterhold. Compatible with ETaC and even adds some, very boring, quests.
Riften Theif Edition - http://www.nexusmods.com/skyrim/mods/31669/?
A overhaul like Solitude Reborn and Sky City, Riften Theif Edition is the best Riften overhaul. Now, if you want to use Riften Theif Edition with Dawn of or JKs Riften, you MUST download this edited esps along with the main file. Replace the main esp with this edited one: https://mega.nz/#!lwpRxCpS!zKv-RyqneNO1dsE9nRgQkn-FKK_ZiSClHWshBetorQ0
This edit was made possible thanks to Mistel of /tesg/.
I highly recommend the edited Riften Theif Edition with Dawn of or JK Riften. The interior Riften worldspace changes it made are not that great, it's the exterior slums it adds that are a must have.
Windhelm Lighthouse - http://www.nexusmods.com/skyrim/mods/35693/?
Not really a town mod, nor is it a must have. It's just a nice little immersion building mod.
Quest mods that add towns:
Moon and Star - http://www.nexusmods.com/skyrim/mods/52397/?
Adds a small dunmer village that has its own quests and a shop.
Helegen Reborn - http://www.nexusmods.com/skyrim/mods/35841/?
Mods that adds new towns:
Legendary Cities - http://www.nexusmods.com/skyrim/mods/47989/?
Adds 10 new towns to the world of Skyrim based on the lore of Arena. Some of them even have quests and custom dialog, while not voiced.
Garvostead - http://www.nexusmods.com/skyrim/mods/71836/?
While Garvostead doesn't look like much at first, its a nice little town at an important crossroad that even comes with its own jail.
Helsmyrr Village - http://www.nexusmods.com/skyrim/mods/64442/?
Adds a very comfy town in the Rift.
Laintar Dale - https://mega.nz/#!4wgQTQwA!Gzsv8q3pW8eUvF3ZdCI15nMs-AinXfuKncLfozzQ2Gg
Adds a small village based on the lore of Arena.
DO NOT DOWNLOAD OAKWOOD. ITS A CTD MACHINE.
SeaPoint Settlment - http://www.nexusmods.com/skyrim/mods/56084/?
Adds a small comfy town in the corner of Skyrim across from that edgy vampire castle. This town has custom music, shops and player home. As well once a week a ship shows up with custom vendors.
Pirates of The North - http://www.nexusmods.com/skyrim/mods/69317/?
Like Legendary Cities, this mod adds a few towns, inns and even a ruin to the world of Skyrim. All these towns are out of the way from major mods and fit in almost perfectly into the world (one town Mitt uses Cyrodilic buildings near Rorikstead). This mod adds new armor and weapons (alright the armor is mostly from Immersive Armors and the weapons are remeshed vanilla weapons), as well as new drinks, food and misc items. It even comes with a boat you can use to sail (fast travel) around Skyrim. This boat will take you to most of the cities in this mod, as well as a few Inns on the shoreline, even a few small docks outside some major cities too.
What's great is this mod is 100% compatible with all the mods listed above.
The only thing to look out for is the usual grey-faced NPC issue, one book has missing textures, and for some reason the fence and static-cheese mesh wasn't agreeing with my personal textures.