Ran the EXE through Admin Studio. I found you can exclude all registry keys. All you need is the Program Files\WinAMP folder. I also removed pmp_usb.dll from "Program Files\Winamp\Plugins" so that users will not be prompted everytime they insert a USB drive, to have WinAMP manage it.
Finally I selected some defaults for the WINAMP.INI by starting winamp, selecting to not associate any file types, changed the preferences for tray icon only, don't check for product updates, and saved out that INI file removing userspecific data by hand. This needs to go in $APPDATA%\Winamp\winamp.ini of your user.