Here is my list, I'll update it when I finish the spirit temple.
"Quick, hide!"
--- Best ---
1)
Spirit Temple:
I loved this temple, not too hard, not too easy, the mirror shield was a great fun, I also loved the Iron Knuckles, they were indeed awesome, but I never knew they could damage you when you were using your shield, so it made me use my darn Lon Lon Milk. >.<
Probably the best mini-boss, I liked the neato tricks with the Mirror Shield, and the Egyptian-like theme. I liked the temple more with Adult Link, and Nabooru (Iron Knuckle form) actually made me use my fairy when I was being careless. D:
Twinrova was sinch, I defeated her without taking damage on my first run-through, but I took a bit of time. Truly a great temple.
2)
The Shadow Temple:
This temple was very scary for me (hey, I finished today and I'm only 11

), which also made it cool, I loved the traps, and more importantly the Lens of Truth and the Hover Boots, I didn't like having to pause the game and change boots, the ReDeads and the stupid Wall/floormasters, I got sent back to the start and I was very angry, so I used Farore's Wind just in case next time. Pretty cool and creepy, as was the boss, that was the second boss that was actually challenging for me in Ocarina of Time (so far), because it made me use one of my fairies. >.<
3)
Dodongo's Cavern:
Eh, you didn't expect this to go here, did you?

This place was pretty cool, and it was not too hard, or too easy, can you believe the hardest thing for me was finding the bombs when they were on a ledge right next to me?

A pretty cool place, the only bad thing was the boss was far too easy, I beat it in like 30 seconds without taking damage at all.
4)
Fire Temple:
A pretty cool place, got me stuck in a few places for a while.
I loved the megaton hammer and the boss, the fire dragon Volvagia in this temple, it was also pretty cool saving all those gorons.
Volvagia wasn't too tough, I owned him without using a fairy, pretty cool temple, I just didn't like the Like likes.
5)
The Bottom of the Well:
One word:
SCARY!
I was a litttle creeped out this morning, and hated all the stupid traps I fell down. >.<
The boss, the Dead Hand, was pretty cool, I was relieved I finally got the Lens of Truth, at the end, a pretty creepy, yet cool mini-dungeon.
6)
Lord Jabu Jabu's Belly:
A pretty whacked out location, but whatever, as long as I get to use a Zora princess to kill enemies, the place was pretty hard, I almost died when I didn't have the boomerang, the mini boss was a bit challenging, probably harder than the actual boss, an alright dungeon.
7)
Inside The Great Deku Tree:
Wow, the first dungeon, WAY too easy, but a good starting dungeon seeing as you only had 3 hearts, the slingshot was pretty sweet, but Gohma was too easy, I liked all the neat tricks in this place.
8)
Water Temple:
Gah, I hated this place, yay, let's go change the water level, yay, let's go find keys, yay, let's own this far too easy boss, NO! I hated this place, the only good thing was the mini-boss, Dark Link, but I still pwned him with the Biggoron's Sword, I really hated this place. Morpha was too easy.
9)
Ice Cavern:
The worst mini-dungeon, I disliked this place, the boss was too easy, the place was whack, it's a shame it was the Ice place, ugh, really bad.
Worst dungeon on my list so far.
--- Worst ---
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and Link's House. Damn, Link's House is hard!
EDIT: I updated my list. You were right, Vergo.