Just finished the game, didn't get 100% but I saved right before the final battle so I can go back and do all that fun stuff.
Overall it's an incredible game. A lot of the criticisms I've heard have been completely unfounded.. just nitpicking things that don't really have an effect on the whole. My few problems were with the lack of importance to money (at least they could've had a bank thing like in MM and something big to save towards?) and the easy boss fights where you stand around doing nothing for a long time until the boss lets you attack him. The music was awesome, especially throughout the final dungeon and boss fights. I guess I'd rank the dungeons...
1. Arbiter's Grounds - Awesome all around, and a great boss fight. The puzzles were challenging, but not in the frustrating you-know-you're-doing-it-right-but-just-can't-get-it way. This was probably the only temple where I felt the enemies were difficult enough and an actual challenge, not just a nuisance.
2. Temple of Time - My favourite point in the entire game was the intro cutscene when you first walked into this temple. Absolutely beautiful and so eerily reminiscent of OoT. Playing the Song of Time throughout was also great, and other than the fairly weak boss fight, no complaints about anything here.
3. Goron Mines - It's been awhile, but I remember parts of this temple and it being quite good. I also remember the Iron Boots noise while walking on the walls being so annoying. Cool boss fight bumps this up a little, but it probably still would've landed here.
4. Hyrule Castle - Well, I just played it, so it might be a little bias, but overall this was a solid dungeon. The music was perfect, the constant floods of enemies were actually a lot better than just running past most of them as in the other dungeons. Good mini-boss fights and a great final sequence, though the 2nd and 3rd phases of Ganondorf were pretty annoying when you couldn't hit them just right. The final swordfight was a bit too long, but still good and followed by terrific cutscenes make up for that a bit.
5. Forest Temple - Again, don't remember too much from this, but I actually liked the idea of the monkeys. Sure it's insanely linear, but it was fun and getting used to the Gale Boomerang at the time was necessary. The boss fight was very cool and that definitely bumps this up.
6. Lakebed Temple - In the middle of this temple I thought "ARGH, this sucks!" and so did a lot of other people, but looking back on it, it was a great concept and was very unique. There could've been a bit more challenge added to some of the water raising rooms, but it was still pretty good. The boss fight was great aesthetically, but not too fun to play.
7. Palace of Twilight - I loved the concept and thought it was perfect length for this temple, but the length also goes to hurt it because it's so much shorter than all the others. The final 2 portions of the Zant fight were very frustrating and annoying, so that really lowers its rank for me.
8. Snowpeak Ruins - As cool as this looked when first entering, it turned out to be very disappointing in the end. The Ball and Chain was just a hinderance, taking up so much time just to kill random enemies and break ice. The boss fight was my least favourite of all, and was incredibly annoying. There were hints of greatness in here, but it seemed very incomplete.
9. The City in the Sky - This one was just so linear that it hurt itself. The Double Hookshots are great, but not when you have to use them 45 times in every room just to get to the next one. The boss fight was very boring, just sitting there for minutes while the dragon circled you, then eventually decided to fly in to be beaten up. The minibosses were like that too, and that makes it even worse.
Keep in mind that when I say "bad" I mean bad compared to the other dungeons. Obviously not all of them can live up to the Arbiter's Grounds, but that's not to say that they are bad, just bad in comparison. I really did enjoy all of them for what they were, though some of them could've been better. I'd like to hear some other people rank these too, just to see how we compare.