For the 3D titles:
Favourite:
OOT - Forest Temple
MM - Snowhead Temple
TWW - Dragon Roost Cavern
TP - Snowpeak Ruins (or Hyrule Catle, can't decide)
SS - Sandship
BOTW - Hyrule Castle
Least Favourite:
OOT - Ganon's Castle (as it's just uses themes from the other dungeons)
MM - Great Bay Temple...
For 3D dungeons I actually really like Dragon Roost Cavern, which is probably not a popular choice.
My least favourite 3D dungeon is definitely Vah Naboris, no doubt about that.
Favourites for each of 3D game:
OOT - Fire Temple
MM - Snowhead Temple
TWW - Dragon Roost Cavern
TP - Snowpeak Ruins...