I finished all the files in Super Mario 64, which makes it 4 times. But this was after I erased all data, and when I had only beaten it about 2 or 3 times. This makes it about 6 or 7 times.
Ocarina of Time is another. I've beaten the game only a few times, but when I was younger, I beat Ganondorf at least 30 times. I've done it in every way possible. I even did it with only the hookshot, and wearing the iron boots. Not such a daring feat now, but as a 12 year old, I felt like the coolest kid on the block.