CraigG is right, If this pausing issue could be eliminated, Project64 1.5 would be almost perfect for the vast majority of games. I have tested 1.5 with many games, many different drivers and on many different computer configurations, and the only thing that removes the pausing is removing jabo 1.5 graphics plugin. Unfortunately every other plugin out there looks, and works like crap when compared to jabo 1.5. Smiff mentioned quite some time ago that he was testing a "modified" version of jabo 1.5 that elminated the pausing problem. Maybe there are other issues with the modified plugin since it hasn't been released yet.
specs:
WinXP, P4 2.0ghz, 512MB DDR, Geforce4Ti4200, SBlive
WinME, P3 733mhz, 256MB SDRAM, Geforce2mx400, SBlive
Win98SE, P2 400mhz, 256MB SDRAM, Voodoo3, SBAWE64