I mean the Sewer Beneath the City or the Ruined Ward is a classic. Though the Ruined Ward needs more love. Big old chunk of the city all wrecked and full of woe and they just put a fence around it and try and stop people from nicking things. Good times.
Here's some other ideas for the dungeon being some fucking dumb :
1: THE ATTICS AND ROOFS : like those medieval towns where they kept building up until the buildings leaned into each other and then insane birds started building nests ontop and flying ships kept crashing into the pile and now up is bad and another civilization might of even been started up there?
2. BIG FALLEN OVER WARMACHINES like giant monuments and colossal colossi. They are place around the city , fallen on the city, and buried under the city. They are full of treasure because the crews manning them were like every army ever and loved to loot.
3. DREAMLAND : if you are awake when the city sleeps , it's an alternate city with bad shit everywhere. and LEWD PEARLS OF THE NIGHT
4. CRAWLSPACES: Dungeon is condition like Rising Damp or black mold , but one that makes impossible amounts of space underneath your house or skirting board. Technically the treasure you drag out of there is a fruiting body that spreads spores but no-one has wised up to that yet.
5. METROTUNNELS: Like big ass underground railways that used to connect citys and overland travel is not an option so everyone is really keen on someone making the trip and clearing them out but you know molochs and shit.
6. THE SKY + MOON : really it's just a big ladder away
7. MANGROVES + SWAMPS: though it's basically a forest right around a city that's awful to log and has shipwrecks in it.
8. SHIPWRECKTOWN: So many shipwrecks they've formed a solid structure around the little island y'all call home. Variants include it's in space and they are spaceships.
9. LORD MAYOR MUD: The old city gotten entombed in mud and the new one is just a couple of 100 people sweeping out some tower rooms at the top. The deep river below is emptying out the very bottom levels and things are getting in below too. So it looks like a hourglass if the top bit was some small boxes and the bottom was a wide bottomed triangle
10. THE CITY IS ON A BIG DISC AND THERE'S REVERSE CITY ON THE OTHER SIDE: both citys keep having groups sneak into the other and steal and fight shit. Both citys are mostly wrecked from this. Good one.
11. BIG TREE: it's a big tree , everyone lives up high in the upper branches go down and it's bugs and rot and rotten gods. Pretty sure this is where Chewbacca came from?
12. GOD : he dead and rotting in the middle of town. He's got stuff in him though.