I've always liked the idea of Penance in Bastion Press' Oathbound. It was a massive city that was constantly being rebuilt on top of the older ruins. So it became this big plateau with layer after layer of ruins underneath. So you've got fully functioning city above, and endless adventure possibilities below. Not to mention that the city above was divided into districts ruled by various bloodlords as well as abandoned disitrcts run by undead. Also, given the basic laws of how to become a bloodlord (I think you need 1000 people within a section to swear fealty to you), it was quite possible for PCs to become bloodlords and interact with the rest of the city in political adventures. Disclosure: I did freelance with Bastion back then, but the original gang came up with Penance, so I feel no shame in giving it props.
However, shamelessly, one area I really liked and wanted to revisit was a small piece that I came up in the original Oathbound campaign setting book called Safe Place. It is more town or village than city, but I always wanted to do more with it. Basic idea is that a large number of dretch are stranded after a demonic incursion goes bad (area collapsed killing most everyone). Psionic caller in darkness eventually forms from the dead demons and citizens and becomes the dretchs' All Powerful Cloud God. Cloud God decides to lure others in by pretending the area is safe for visitors and only killing a certain percentage of them (in ruins under Penance monsters pretty common and no one will miss a few dead people). Old sign even remains saying "A safe place to live" with town name gone.
After a while, some of the dretch - more chaotic stupid than chaotic evil - actually buy into the lie that the town is a safe place. So when PCs arrive, they can take part in a revolt against the Cloud God by a bunch of dretch who think it is corrupting what Safe Place is all about. I had all kinds of crazy stuff in there with this town completely run by really dumb creatures - some of whom just run it to lure in people to torture, others who actually try to accommodate and help travelers. I had a lot of fun with it.