The only problems I've noticed mostly seem to be plugin related:
1 - Banjo Tooie, if you watch all of the demos through from start to the last one at Jolly's lagoon with Glidemk2 it'll freeze midway during this demo, whereas with Glide or Rice this doesn't happen.
2 - Chameleon Twist 2 - doesn't matter which of the three plugins I use, I don't get any sort of picture other than a black or white square box.
There is also a game or two that refuses to start (the original Chameleon Twist for instance) due to not supporting the controller pack. In most cases this is something that'd we'd want enabled, but for this game and a few others they simply function incorrectly if it's present. A toggle or an automatic game detection / turn off might be something to look in to.
And lastly, I don't have any real graphical problems or sound problems (especially if I capture to avi, I commend you on making this pretty much flawless) except in one or two cases. For instance in Banjo Tooie, if I were to play (or even play and dump to avi) the opening movie works without a hitch, but if I run the second movie there's clearly something slightly off about the audio and video as if they're out of sync. This is present on any throttle with any amount of frame skips, however generally I set frame skips to zero and the throttle to clock throttle.
Here's a savestate for Banjo Tooie (U), with all the movies unlocked to show you what I mean:
http://www.mediafire.com/?1brm22m9ae2bfgd
All the roms in question were the North American ones.
I'm pretty sure a lot of what I mentioned is either previously known (whether towards Bizhawk or Mupen) or has an easy fix I'm overlooking, but I figured I'd post with as much information as I could just in case!
