Direct 64 doesnt work on ATI radeon cards (also considering we both have the same graphics card). Basically 1964 should work much better for you, in particular for higher system spec. required games, such as Goldeneye. PJ64 can be a little sluugish with a 1.02 Ghz processor.
EDIT: I forgot to mention to use Project 64's default plugins. For 1964, I recommend using Azimers audio plugin, Schibos is good, especially if youre having trouble with speed, but Azimers has better quality (or so I think). As for the Input Plugin, N-rages works best, however I have been more comfortable using Jabos Direct Input (just my personal preference).