I'll go ahead and list some of the ones I can remember.
- The Lanayru Mining Facility.
I had a ton of trouble figuring out how to defeat the Sentrobes.
http://www.zeldadungeon.net/Zelda14/Enemies/Sentrobe-Screen-Small.jpg In fact, at first I thought they
couldn't be defeated. It took me a while to blow the platform back and forth while avoiding the first Sentrobe in the dungeon. The next time I came across one, I got irritated with it, and decided to call Fi for advice on how to defeat it. Thanks to her help, I finally figured out how to get rid of those pesky Sentrobes.
- Playing the harp duet with Kina in the Lumpy Pumpkin.
I don't know why, but this is the only time I ever have trouble playing the harp just right. In fact, I'm still kinda poor at it. I've only ever gotten the best reaction twice. I usually end up with the third best reaction. That's still good enough for the Piece of Heart, thankfully.
- Sky Keep.
This was really hard for me, but I'm actually glad it was. I love Sky Keep! Despite it being incredibly hard for me the first time I tried it, I couldn't help but admire its difficulty. It's got to be the best challenge in the game, in my opinion.
- Fledge's Pumpkin Pull.
I can't begin to count how many times I wanted to rage-quit. xD I kept telling myself, "It's for that last Piece of Heart! You can do it!" It didn't make it any less challenging, though. That Flege sure is a tricky fella, especially when he starts throwing the pumpkins way off to the side, near the wall past the Sparring Hall. That part always gets me.
- Dodoh's skydiving minigame on Fun Fun Island.
The actual name of the minigame escapes me at the moment... One thing I like about it is that it's basically all up to luck. Unfortunately, I'm not typically lucky. ._. This really took me a while to complete, but it was worth it, getting that Piece of Heart. However, this still wasn't as hard for me as Fledge's Pumpkin Pull.
Those were the hardest parts of
Skyward Sword for me, to the best of my memory.