They're really equal, being both based on Zilmar's plugin spec. Cpu core is basically perfected in both, with major issues really lying in graphics and sound plugins. I personally prefer PJ64 with Rice's plugin & D3D Pixel Shader combiner, Jabo's Audio, and NRage's input. PJ64 just had a major new release after much silence and supposed death.. 1.6 is fabulous. 1964 0.9.9 was released on Jan 3 of this year, so it's not outdated by any means. Both incredible emulators, the two very best.
Due to the heavy optimization of 1964's Dynarec core, it's typically faster than PJ64, but if you have a 1.2GHz+ system, that shouldn't matter.
