SIDS are definately chiptunes. Most MODs are not true chiptunes. :-D
MODs are music files that contain pre-recorded audio Samples (8 or 16bit usually) and tracks (MIDI note like data ).. so you have 'trackers' to create songs.
SIDS are songs that use the built-in capabilities of the sound chip (FM synthesis usually) generated in realtime.. hence 'chiptunes'.
OctaMED Sound Studio is cool because you have the capabilities to create MOD type songs that include synthesized instruments (though somewhat limited). You could actually create an OctaMED song that was all synthesized instruments, hence a chiptune. :-D
heh.. and I don't have a favorite chiptune at the moment cause I like of the ones I hear. :-D
Because of my work schedule and so on, I haven't had a chance to look at this:
http://www.arts-project.org/(If you have more time than me, please check this out and tell me what you think, we might want to port something like this)