I'd delete all folders that aren't filled with stuff you put on there...ie don't wipe it and lose your music, photos, videos, apk backups, etc.
Deleting all the other clutter wouldn't hurt. The necessary folders and contents will be recreated when they're needed.
I also Odined my phone back to 2.1 factory out of necessity before updating with the zip. I don't know if it helps performance any, but it's nice to know that it's clean.