While sitting around in our small liberal arts university dorm, someone played this song. Using our highly developed skills of postdeconstructionalism we realised that this song is actually a metaphor for religious strife. This is somewhat different from Alias Mother Jonez's conception as all Men represent religions rather than simply cultural institutions. Allow me to explain...

Triangle Man
is clearly Christianity as represented by the Holy Trinity; you may wish to extend the metaphor to include Judaism and Islam if you see them as united in hatred.
Particle Man
represents Buddhism (or all Eastern religions, if you like), this is evident from the koans in the second verse. Particle Man does not represent science because these are very unscientific questions; also it seems unlikely that anyone would still believe that Christianity will "win" against science.
Person Man
is atheism or humanism1. Clearly TMBG are theistic2 by their belief that atheism leads to depression.
Universe Man
is the most difficult Man to interpret. I believe that He is either God as absent from all religious spin, some kind of deeper religion than all currently practiced, or else something beyond religion like science. Clearly, unlike Triangle Man and Particle Man, Universe Man is universal, as well as being kind (a hybrid or superset?) to "lesser" religions. Finally His watch suggests that He is either timeless or still destined to arrive (at least to our corner of the universe).

1: ((human = person) ⊃ (humanism = personism)) ⊃ (Person Man = humanism)

2: I was unable to verify this hypothesis, therefore from my point of view if I learned that TMBG were theistic or, even better, Buddhists, I would consider this evidence in favour of my interpretation of this song.