My favorite Oot side quest was the Biggorons Sword trading sequence. I liked how some items were timed but I do wish there were more timed items and that the trading sequence was much longer. I found it interesting because you got to see different items in the game and the fact that you actually got a usable sword at the end of te side quest!
I always look forward to the Biggoron sequence whenever I play through OoT. I love challenging myself to beat the clock and wind up with an awesome weapon.
If were counting every heart piece as one quest I gotta go with that. Easily the most variety there. Some require mini-games or quests, others exploration. The variety alone wins it for me. One thing I look forward to every Zelda game is heart piece collection because of those very reasons.