Here are some of my favorite dungeons (in no particular order):
Desert Palace (ALttP)
Ganon's Tower (ALttP)
Forest Temple (OoT)
Stone Tower Temple (MM)
Jabu-Jabu's Belly (OoA)
Dark Hyrule Castle (TMC)
Goron Mines (TP)
Lakebed Temple (TP)
City in the Sky (TP)
Temple of the Ocean King (PH)
Tower...