I think an excellent rendition of the standard dungeon is done in an urban area, especially the flea-bottom labrythine back alleys of the poor district. The alleys themselves serve as the passages and larger court areas (market squares). While the entrances to the various buildings serve as dungeon chambers. Mix these with canal systems, stairs going up to gallery levels over the alleys and you have a very much 3D dungeon without a roof. Of course sewers beneath accessed from drains at ground level can serve more as the dungeon tunnels beneath as well.

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