My name says it all. I like Mupen64 because it is very open sourced, ported successfully to multiple systems and platforms, and is the only N64 that has a built in AVI recording system.
I know ow you feel, that's my preferred N64 EmuI'll have to go with PJ64 since I found it the easiest N64 Emu to use and setup, and it's the Emu I spent the most time with.