Not Included mini dungeons and Ganon's Tower,Moon etc.
Best
5.Goron Mines(Twilight Princess)
why:its a nice temple(overall)
4.Snowpeak Ruins(Twilight Princess)
why:You play in a mansion what else do I have to say.
3.Water Temple(Ocarina of Time)
why:because of the awesome puzzles this temple had but I never got stuck on this one and the second best music from OOT is in this temple.
2.Spirit Temple (Ocarina of Time)
why:great atmosphere and youhave to play as both young Link and Adult Link and the bestmusic from OOT is in this temple.
1.Stone TowerTemple (Majora's Mask)
Why:Best overall puzzles and one of the best Zelda music is in this temple.
Honorable Mentions
ragon Roost Cavern(Wind Waker) and Woodfall Temple(Majora's Mask)
Worst
5.Earth Temple(Wind Waker)
why:It was just boring
4.Snowhead Temple(Majora's Mask)
why:just too long IMO and boring
3.City in the Sky(Twilight Princess)
why:TOOOOO long and very boring
2.Shadow Temple(Ocarina of Time)
why:I always get chills when I am in this temple and good thing this temple is the easiest of the 5.
1.Great Bay Temple
why:I dont even wanna talk about this one took me 3 hours to collect the damn stray fairies and playing with annoying currents.Only Zelda temple that gave me real troubles.People say Stone Tower is hard but this is the hardest temple(Stone Tower is damn easy IMO)
Honorable Mentions:Forest Temple (Ocarina of Time) and Tower of the Gods(Wind Waker)