Definitely the pumpkin-toss archery in Skyward Sword, the reason it was hard is because you needed the screen to scroll to the side, but that could only be done my pushing it with the cursor, but then you need to the cursor to aim the arrow so you can't do both at the same time so aarghjaghsgdkSKADGASLG!!
Seriously, if it just scrolled by itself or you could simply scroll it with the joystick, but noooo.....
Also, the tattooed fisherman's island-jumping torch game in MM, just because I had no idea it even existed, and I think there were several obscure things you had to do to activate it, including riding on a boat that, IIRC, didn't look like it could be interacted with.
EDIT: Sometimes it takes a long time to dig one up in LttP. Also I think I vaguely remember it being hard to get one from the mole-like person's mini-game in SS.
Edited by Cukeman, 10 March 2016 - 08:32 PM.