Vivec expansion made Vivec my favourite city, it added a lower seedier underbelly of shanties and shacks with hastily erected rope bridges and boats.
There is also the boat mod (not sure its name) and that adds a fully controllable boat to the game, its spectacularly awesome but prone to occasional crashing. But nothing better than sailing solo from Ebonheart to Dagon Fel or Solstheim. It even has a launch for landing and is a pretty good house as well (as the boat interior).
Those are the ones that really stand out for me, I did use a lot of minor mods, such as one to remove the glow from enchanted objects. Get the expansions if you haven't already got them.