My picks:
Bluffside - in my opinion, one of the best all-around fantasy RPG cities. Fun and imaginative.
Hollowfaust - this is one of the more interesting fantasy RPG cities I've seen. A city run by necromancers - and it's not evil. In fact, the citizens actually have it pretty good. A very interesting setting. This could make for both a good place to set city adventures, and a very unusual choice for PCs to use as a home base.
City of Splendors - This is a boxed set for Al Qadim. It's a very richly detailed city for an Arabian Nights-style campaign. One of my favorites.
Free City of Haven - one of the earliest RPG cities. Tough to find. It's a gem, though. Very detailed, and "feels" like a living city. The downside, besides its scarcity, is that it was never finished. The material that was finished, though, is more than enough for an entire city on its own.
City State of the Invincible Overlord - the granddaddy of RPG cities. Very, very quirky. Very fun, very dangerous.