ok, brother. you asked the right guy on this one! i'm a classically trained musician myself, and I'm currently working on a small book about the musical semiology that is peculiar to masonic ideals that may be found within a close Roman numeral chord analysis of works of a Masonic nature, and how those new musical symbols have come to affect the practice of composition in the time since. (for a teaser, the theme song to "Cheers" uses the same musical symbolism as Mozart in order to communicate the concept of brotherhood)
Mozart is great, and The Magic Flute is a wonderful example of some of his masonic work, but he also composed music for a couple of Masonic funerals, a Masonic Cantata, and some other works specifically for the lodge. Much of the music Mozart would have composed for the lodge would have been improvised at the keyboard during the degrees/etc.,
Sibelius also wrote a lot of masonic music, as did Haydn.
honestly, if you're interested in the history of these masonic composers, I'd recommend this site...
http://www.masonmusic.org
it gives a pretty comprehensive list of the overtly masonic compositions of the above mentioned, plus a pretty good list of other musicians/composers who were masons, and may or may not have snuck masonic ideals into their work.
here's a couple of mozart's non magic flute, but still masonic works:
http://www.youtube.com/watch?v=--sDBQuz6DY
http://www.youtube.com/watch?v=MwsWQerNGjo
http://www.youtube.com/watch?v=TF4vQ8fBkVg&feature=related