I've only done a few of the sidequests in Skyward Sword, but of the ones I have done, my favorite is Fledge's Confidence. Although it could get somewhat boring at times - with having to constantly switch from day to night and whatnot - it could be rather humorous at times. Also, I enjoyed watching as Fledge's strength and confidence progressed, because who doesn't love the underdog?
And the minigame unlocked afterwards was fun. Not only that, but it allowed you to gain back the Rupees you spent on all those potions you bought him.