I haven't beaten the game yet, but so far,
Eastern Palace
House of Gales
Tower of Hera
Hyrule Castle (dunno if that counts, but I'll stick it here anyways)
Thieves' Hideout (my favorite dungeon yet)
Dark Palace
Turtle Rock
Skull Woods (good dungeon, but its my least favorite only because of mummies and darkness eep)
Honestly I'm just doing them in order of which one I end up closest to.
Eastern Palace
House of Gales
Tower of Hera
Hyrule Castle (dunno if that counts, but I'll stick it here anyways)
Thieves' Hideout (my favorite dungeon yet)
Dark Palace
Turtle Rock
Skull Woods (good dungeon, but its my least favorite only because of mummies and darkness eep)
Honestly I'm just doing them in order of which one I end up closest to.