N64 emulation is still in the growing stage, and you need a fast computer (and preferably a 3D accelerator) in order for it to work well.

Project 64 Homepage This emulator is amazing. It's actually easy to configure, and it runs many games (including OoT and MM) perfectly! Highly recommended.
UltraHLE Homepage

Download from Zophar.net

The first N64 emulator to run commercial games, this project was abandoned and started up again. It's good all-around, but it runs on Glide and so requires a 3DFX card or a Glide wrapper. I've found that this is one of the few emulators that runs Zelda 64 correctly!!
Daedalus Homepage This promises to be a very good emulator. It's compatible with many games, and it will tell you if a game is going to have errors or not. This emulator will run both OoT and MM, but not very well.
Nemu64 Homepage A very compatible emulator. It will work with any 3D accelerator since it uses Direct3D, and with any joystick since it uses Direct Input. Sound emulation is excellent, but I have trouble reading in-game messages sometimes.
Corn Homepage This emulator is very fast but tends to be unstable for some people. The sound seems to be out of synch with gameplay a lot (maybe it's just me, though).