My daughter recently appeared in "Godspell," 25 years after my own performance in the show. In the course of her rehearsals, I learned something new.
When I heard them working on "Prologue" and "Tower of Babel," I asked the director if these were something new. He explained that they were not usually done in productions because of their complexity. Furthermore, the track list on the CD is different from the complete score because the producers wanted the cast recording to have more of a "rock album" feel, so they left out those two tracks and started off with "Prepare Ye" followed by "Save the People."
Having said all that, my fave songs in the show would probably be (in no particular order) "Turn Back O Man" (for reasons already given by others), "All For the Best" (same here), and "We Beseech Thee" (probably for its infectious quasi-Bo Diddley beat, among other attributes).
A great show, still hugely popular after all these years, and boy does it ever piss off the religious right. (Another strike in its favor).

Pooby