My most recent dungeon (under a city) has 4 levels. First level is the defunct sewer system. 2nd level is an abandoned thieves guild. 3rd level was the living/entertaining quarters of the guild's wizard. 4th level was the wizard's laboratory.
I like it because each level has it's own distinct flavor: first level is full of dire rats and giant spiders, 2nd level has traps, 3rd level has weird magic stuff (attacked players with an animated cabinet, they had a hard time believing it was real...) and the 4th level has truly fantastic and bizarre stuff.
None of the levels was completely explored, because the players goal was to loot the lab.
PS