I mainly use Project64 because it's stable and runs at a fair speed for me. When I can be bothered to risk it, I'll use 1964 because it's a tad faster for me. The only thing is that it crashes fairly often and doesn't have the same savestate support that pj does (making it a pain to use with Glide64). I still use Ultra/SupraHLE for GoldenEye and a few others too, cos that thing runs like a bitch on heat
IMO it's all apples and oranges. I'd probably use Nemu too, if my dodgy graphics card didn't make it roll over and die
