SSF is probably the most full-featured Sega Saturn emulator out there. I'm not sure if it's opne source, but from what I can tell, it doesn't appear to write any values to the registry. The only problem I can see with it's portability is it does not support relative paths.
Official Homepage: http://www7a.biglobe.ne.jp/%7Ephantasy/ssf/index.html
English Translation: http://evilboris.sonic-cult.net/SSF/index.php?x=download
Maybe a wrapper is all that's necessary?