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.
This is tough for me. As I found a majority of these side quests rather annoying. However, I voted for Cawlin's Love Letter, because in both ways it's entertaining and sad, because either way you go....Cawlin ends up either completely heartbroken, or every night tormented of this ghostly hand caressing him. LOL!!! And just the idea of giving the love letter to a hand that comes out of the toilet is incredibly disturbing yet hilarious at the same time!
I thought the unwanted admirer one was great. I kind of messed up though, I meant to tell the item check lady I didn't like her like that but when I got to the dialogue I felt really bad about it and didn't go through with it. I hate being mean and letting people down, how could I break her heart like that
But I still felt bad...I mean what if Zelda found out? Woah is Link.
Finding the rattle was definitely my favorite. It was the hardest for me, because I had no idea where it was, and then I kind of forgot about the side quest, until one time I just found it after diving off the waterfall and I thought "Oh, I forgot about that!"
I really liked unwanted admirer. I just found it hilarious how she started off so cold and bored and then steadily grew to like Link. However, my favorite part is what she says after you turn her down, and continues saying every time you talk to her (I would put it in the spoiler drop down thing, but I don't really know how)!
I enjoyed the Horned Colossus Beetle sidequest the most. The majority of the sidequests were just going back and forth between people to talk and advance, or using dowsing to find something that someone wants. Beedle's sidequest made you complete a challenge that is somewhat difficult (at least on the first few tries).
Also, I think that you should add Pumpkin Landing to the options. It wasn't for gratitude crystals, but I think it would still be classified as a sidequest.
I like the Unwanted Admirer one...but it would have been more interesting if the relationship was already there at the start of the game, and to see a conversation between Zelda and Peatrice. Awkward much?