I really only hated the water temple because of the confusion of the raising and lowering of the water. I think they should have made the levels a bit more distinct, so you knew which level you were on. I dind't find the map too helpful in the main flooding chamber. Otherwise, the outskirt rooms were fine!
For me, I think my favourite temple, oddly enoug, is the Great Deku Tree. This was the first 3-D Zelda dungeon that I ever had to battle through, and it was wild to see what they were able to do in the third dimension. I know other temples had other great moments in them, but the thing I will remember most was having to jump from very high up in order to break the spider-web to get to the lower levels. Even doing it form one level up wasn't enough to break it, you had to really get some altitude! Once I figured out what I had to do, it clicked as to the potential that games in 3-D had, and it amazed me.
This might seem odd to newer players who grew up with 3-D gaming, (suddenly, I sound so old...) but when you grow up with 8- and 16-bit, then something like this comes along, it's pretty impressive, and memorable. That's why the first temple in OoT will always be my favourite.