I have beaten the classical game, The Legend of Zelda Link to the Past about 20 times. A majority of them being on the original Super Nintendo Entertainment System and the rest on the Gameboy Advance remake. It was just so addicting to try and see how many items or rupees one could collect before the next dungeon or so.
Link to the Past, by far. I've beaten it maybe 20 times now and it's the only game I can beat 100% completely blindly in ~3-4 hours (the world record is around 1:50 IIRC, maybe one day I'll be aiming for it )
Hmmm... I think PH is my most beaten game. About 5 times I think, & TP is a close second with 2. Once I beat them, I don't revist them for a fair while unless something sparks off in my head, telling me to go replay it again.
Either Majora's Mask or Ocarina of Time. I've lost track of how many times I've beaten those two. I've beaten both 100% and beaten Ocarina of Time with three hearts. I plan to do so with Majora's Mask but I haven't gotten to it yet.