This is a top thread, given me some ideas to think about for my own drum and rhythm programming! I just want to address one small thing in the very first post ... which comes around also to maybe have some relevance the last few posts as well.
I've always wondered how, in reggae, the listener can 'tell' that the guitar/organ chords are on the offbeat, producing the trademark skank. Surely this would depend upon there being an incontrovertible 'marker' of the beginning of the bar? Do we simply attribute the bass drum (which may be felt more than heard in many contexts) to the beginning of the bar automatically? And would someone who had never heard any music before automatically do the same?
You know, I think the key here, and sorry to take the emphasis away from the rhythm for a moment, but the key here are the CHORD CHANGES. Yes, reggae has chords. ;-) It's fairly typical even in reggae to change the chords on the one, even over a fairly skanking beat. Chord changes aren't all on the bar of course - it has plenty of passing chords just like any good Beatles song.
But the major chords, that define the key you're singing and playing in, typically in reggae change on the bars (or on the one and the three).
As someone pointed out just above, the vocals in songs often don't start on the bar, but if you listen carefully to the vocals even in isolation, you can hear where the chord changes are. This would typically (but not always) define where the "one" is. Think acoustic guitar and singer territory. Reggae is easily played in that form (and still generally recognisable as reggae too I might add).