I don't know if it's just me but every time I press start to enter the menu it takes a few seconds to load. I wouldn't want to play the water temple like that where you're constantly equipping the iron boots. Although I'm only playing Zelda as a test, I'm waiting for the 3DS version really to play through it yet again.
That is a common problem in OoT on emulators. Project64 had a cheat for this in its cheat database. If you didn't turn it on it took even longer to open the inventory than on the pandora (it was about 30 seconds i think).
I just recognized, that some textures won't load when i enter a building (e.g. the Kokiri-shop). There are just yellow surfaces all around. The models are looking normal though.
Oh, yeah, almost forgot: the game appears a bit dark and i can't get the screen brighter (it's already set to maximum brightness). Same thing happens in Dega, everything else is OK so far.
Maybe someone can give me a little help here :unsure: