1964 has a few fixes to a few games that still bug PJ64... here's a list:
1.Rat Attack(U)- PJ64 for some reason runs hella slow... but 1964 runs great!
2.Donkey Kong 64(U)- PJ64 tried to supply a work around with the polygons poping out all over the place (Audio syncing the game)... it still exist though. 1964 has no problems whatsoever, give it a try and you'll see

!
3.International Track and Field 2000 (U)- PJ64 has slow downs everywhere in this game... as for 1964, it runs the game... as i said before... perfectly!
4.Misc. Games run better on 1964 than PJ64 and it also has internet play.
Now don't get me wrong, I'm still a huge fan of the PJ64 Emulator. I just recently joined the forums to help with the misc. problems that occur with some of the games/roms that run via on PJ64/Beta RDB/plugins. I only use 1964 for only 3 games, which i numbered above (points 1-3) ...