Forest Temple
I really have to say that I did not enjoy this Temple to much. It felt way to much like a lame opening Temple, which is supposed to get you used to it. I suppose that is what it was designed to be though. I also did not like how long it took you from the beginning of the game to get to the temple. Basically the whole part from the very start of the game to after you beat this Temple felt long and boring, which is never a good start to a game. I also hated collecting the monkeys.
Goron Mines
I really liked this Temple, actually. It probably places second or third on my list of the greatest temples ever. It had a very unique design, which was quite nice. And meeting all of the Goron Elders was a great idea. Plus the Bow is an excellent weapon for this temple. But as I never really liked fire temples to much, this cannot be my favourite. Though I do say this is where the game really starts to pick up. During and right after this temple.
Lakebed Temple
This Temple felt like a milestone. Which it was really. It gave you a very useful item, and set you forth for the next, more plot pushed half of the game. It does the job well, but annoys on the way. The boss is pretty cool though. The Temple really gave you the feel that you where deep underwater where no human should be. No human or Zora, because the place felt kind of non-templey. But yeah. It was still a good temple, through and through. I can't say I liked the design much though.
Arbiter's Grounds
This place is as hard and scary as hell. I really did not like this place the first time I played through the game. The layout is quite confusing and annoying, with no real pattern, and overall the Temple felt pretty short, but I still liked it. Kind of. The boss was pretty fun, but I can't say that I approve of the item. It does fit the Temple, though. And the introduction to the Mirror and the backstory about Ganondorf and the sages is pretty good.
Snowpeak Ruins
Now this is my favourite Temple. It's really a place I can get behind. It feels comfortable, whilst still giving you the edge of danger and exploration. The idea of going out through little mini journeys to get the items was pretty awesome. And the soup was funny, and a nice little boost. The idea of the canons was pretty good, and the mini-boss and item were awesome. The layout was excellent as well. It really felt like a beautifully constructed Royal retreat. The on thing I did not like was the boss, however.
Temple of Time
This temple felt way to linear for it's own good. Though it was cool how you felt like you were climbing a great tower, with all of the floors it had. Controlling the statues was very fun, and the mini-boss was a great introduction to Dark Nuts. The item of course is fun. I mean. Come on. But the way you just went down the path to get the Statue, and then came back felt kind of boring. And the boss was unfitting for the Temple. A great, ancient Hylian Knight Guardian would have done the job much better.
City in the Sky
I can't say that I remember to much of the temple. I just have to say that it was generally a not so fun experience. And it had an awful layout. While the item was useful, it felt sort of tacky and not so well thought out. They could have done something much more innovative and interesting like with the last few temples. The mini-boss was lame as well. I think they could have thought of something better. The boss however, was the best in the game. It was pretty epic.
Palace of Twilight
Now this is what not to do with a Temple. Don't give you an item, make it short and rather easy. Do not use any interesting ideas, make the boss very lame, make it a huge let down to finally getting to go to a fabled place, and finally make it not make sense. There you have Palace of Twilight.
So, overall here is my final list.
Snowpeak Ruins
Goron Mines
Arbiter's Grounds
Lakebed Temple
Temple of Time
City in the Sky
Forest Temple
Palace of Twilight.
And that is in order from favourite to least favourite.