Having played the game many, many times, I can now get to 99% or so without a guide, but I inevitably forget a handful of skulltulas, I usually give up on the biggest quiver upgrade after failing the horseback archery mini-game 50 times in a row, and I don't attempt to catch the Hylian Loach anymore.
Used to hate catching the big poes, but when you know where they hide, it's pretty easy and fast. Only the one near the Kakariko entrance still annoys me.
I got EVERYTHING on there. EVERYTHIIIIIING. XD I just... I have this OCD, where if I play a file that's not 100% completed, I can't sleep. Honestly. But otherwise, I believe the ONLY Zelda game I haven't 100% completed is Wind Waker. >> Those treasure charts are eviillllll~