System specs... details... details we need details (CPU speed, graphics card, sound plugin, Operating System, Memory installed). As a general rule, none of us on this board are clairvoyant.
The problem you are having is, your computer isn't fast enough to give a constant 50 or 60fps in Goldeneye (a game that requires high specifications). The sound will always tend to stutter when you are not attaining a maxed out framerate constantly.
As a start though, you should use 1964 - as it is the slightly faster emulator for Goldeneye.