It never crashed on me whenever I borrowed my friend's N64 copy. When I tried playing the Collector's Edition about a month ago, it crashed on me literally 8-10 times. It bugged the crap out of me because I had collected so many things. I also noticed the crashes come more frequently if you save at an Owl Statue and continue playing later which I noticed happen sometimes before.
I'd like to get it on VC though because I don't have the original game and I'm getting tired of the game crashing with the GCN version and playing on an emulator doesn't have the same feel as if you were playing it on TV. I love the GCN controls though which is an upside for me.