I've always wondered this too... I read a few months back a similar thread. The version nuumbers relate to real game version numbers. Therefore a higher number is usually a bugfixed game. So, 1.2 should be better than 1.1. BUT, that doesn't mean it works better in the emu. You'll have to check ini notes or just try them to see if they both work.
PJ64's RDB by Smiff is an excellent database of game specific issues etc. Be sure to try that out first. Anyone else want to comment.
To be honest though - All i really care about is Banjo Tooie. I'm pissing my pants in anticipation of playing this game !! Wait wait wait.
