Only a few plug-ins actually support PD. Use Jabo's D3D6 1.5, its not perfect, but it appears to be most accurate and is also the fastest.
For Goldeneye, again Jabo's plugin works the best at the moment, but will soon be overtaken by both Glide64 and Rice's Daedalus. Might want to use 1964 for these games due to high system requirements.