Here is a link to the latest interim build of BizHawk. I have been using it to map Super Mario World, and so far it is working pretty good. The main thing to do to prevent crashing is to not open up the graphics debugger window while the emulator is paused. As long as you stick to that it should work good.
Here is the download link to the version I'm using.
http://code.google.com/p/feos-tas/source/browse/trunk/BizHawk.zipAlso there is an on going thread at:
http://tasvideos.org/forum/viewtopic.php?t=13464So you can offer your input and suggestions for the emulator there. They have already added several of the features I have requested to make mapping games easier. I think it will help if they know I'm not the only person that uses their emulator to map games. So please request some good features from them.