Over at the Hill Cantons blog, there's a couple posts about constructing something resembling the Jakállan underworld (from the Tékumel/Empire of the Petal Throne setting.) I only paid half-attention to it, because I was thinking of it as a Tékumel-centric process. But really, the basic idea has some appeal. In real-world history, cities often get built on top of cities on top of cities, and later excavations may turn these into sprawling underworlds. Traditional D&D underworld design has moved towards small excavations (micro-dungeons) or constructions in large natural caverns (the underdark.) The megadungeon has resurfaced, but we tend to conceive of these as just a bigger version of the micro-dungeon.
I have the inkling of a thought: what about applying the exact same rules used for on-the-fly city adventures to ruined undercities? Maybe with some rules for creating connecting zones?
I'll have to think of this more.