I find that the Fire Temple is usually a very fun playthrough. I'm not quite sure what makes it so enjoyable, but it may just be the general layout. I like the puzzles that vary in level from time to time. The Water Temple had some extreme level puzzles, but I personally found the Water Temple just more tedious than fun at most points. The Fire Temple threw a few things at you here and there and was generally a fun place to explore. Very wide, lots of places to go, just kept you on your toes and prevented you from being bored.
The Spirit Temple used to be my favorite, but that may have been just because of the utilization of going back and forth through time. The temple itself had some mediocre puzzles. It was pretty linear for the most part, it just took a little bit of looking around in the large room to find a few markings and switches here and there. It wasn't exactly anything special. The Fire Temple is quite a bit different from it in that there are so many different places you can go at any given time, and though if you check every part of the temple at least once you'll be able to advance, it's still a lot more enjoyable than just being able to go through and do it all step by step.