My favorites are:
Every dungeon from MM, even great bay.
Spirit temple (Oot)
Dungeon 7 (LoZ)
arbiters grounds (TP)
Snowpeak ruins (TP)
Goron mines (TP)
Thieves Town (LttP)
Earth Temple (WW)
Most dungeons (SS)
As for my least favorites:
Jabu Jabus belly (OoT and OoA)
Water temple (OoT)
Lakebed...