Freeport!
Are you kidding?! Freeport is without a doubt the best city I've ever used, and I've used quite a few. Freeport was originally just a stop for the first modules in my campaign, and now I can't get my players out of it (nor do I want them too.) The book and the NPC guide have so much to offer that I could campaign in Freeport indefinately. I use the newspaper as my newsletter, I have the players commonly encounter the town politics and characters with ease. I love Freeport!
As for other cities that I have used to good effect. I really liked Tredroy for GURPS (my book, sadly, was lost when my car died years ago, alas.) I would love to see a d20 version of the Citybooks! Perhaps a best of book should be done.