There are three causes I can think of for this kind of thing:
You do not have Sync Game to Audio checked in your audio plugin configuration, or you are using a retarded third-party audio plugin. The two audio plugins I recommend are Jabo's DirectSound and Azimer's Audio HLE v0.56. Azimer's has less crackling if Sync Game to Audio is unchecked for both, but for games like GoldenEye 007, you want to use Jabo's. The Nemu64 emulator also has a damn good audio plugin....
Your system. I don't know much regarding this, but if you gave your system specifications, more could be interpreted about your problem.
The game. You are probably experiencing a loss of speed in your game or have the Speed Limiter in Project64 off.