I normally use a homemade city.
If I were going to use a premade city, well.. my favorites are all out of print, for the most part.
City State of the Invicible Overlord. Very well done.
Sanctuary.
Pavis (from RuneQuest).
Carse (in Midkemia; based on the real-lfe Medieval Caernovon)
The stuff in Cities of Harn.
I really like the stuff in Seven Cities, for the descriptions, the adventure seeds, the building maps. I can even look at the city maps if I don't do so on a full stomach. There's a reason for that...
I don't own most of the city sourcebooks I've seen for 3E. I have.. strong issues with the maps for almost all of them. All the ones I've seen (save, I think, for Freeport) are done in the 'Buildings never touch each other' style prevalent in the early Forgotten Realms books. It's kinda OK, when you're presenting it as a 'we just want to show the major streets' abstract. It's quite another to take it as literal fact, as most city supplements do.
I'm not a huge fan for 'gritty realism' when I'm playing in a fantasy game, but there are limits. That's one of them.
I might someday get Freeport, but.. probably not. I hate the sharp-edged hard-to-read looks-like-it-was-drawn-on-a-computer city map. but I might be able to put that aside someday. Normally, art will not cause me to buy or not buy a supplement except if it's a city supplement. Then, the map that is presented to me must be well-done and believable.
Another small gripe while I'm on it. A drawing of the city (Iron Kingdoms, that Gygax city book, a couple others whose names do not leap to mind) is NOT a map of the city. It's almost worse than having no map at all. It's useless. Stop doing it.
OK, one other thing even more useless: A thing that looks at first glance like a city map, but is not. A 'map' that shows the fronts of buildings along the street may seem cute. It's not. A 'map' that combines street-map-like map but has pictures or little drawings for the major features instead of that feature's plan.. stop that.