Dungeons are (in theory) built by intelligent people for a reason. There needs to be distinct working, eating, socializing, farming areas. There needs to be wider or thinner pathways between areas based on flow of people & goods.
A good starting place to look for amazing looking dungeons is to look at people who play Dwarf Fortress, and how they build & organize their forts, which are essentially dungeons.
Here are a few good links:
http://discourse.stonehearth.net/t/slave-to-armok-god-of-blo...
https://leelubutterfly.wordpress.com/2013/01/01/dwarf-fortre...
etc. just google image search for "dwarf fortress" and you'll see a lot.
Good algorithmic dungeon design should take into account some of these factors, like good city design would.