I've always preferred the Atari800 version of the theme song, because it had an extra layer of harmony to make the sound fuller.

http://www.youtube.com/watch?v=2EubKmtFBXY

Listen at 0:45, for example--there's that middle voice doing the triplet rhythm in between the bass's quarters and the straight eighths up high.  I haven't heard that captured in any of the modern remixes or updates. 

The version of the theme included with 1.2 is nice, but it could be that much better with the extra harmony!