Nefertiti (Mana Khemia) vs. STIGMATA (Mana Khemia) - Easy. Nefertiti is very good and all but it isn't Godlike.
The Fate ~ Cluster Amaryllis (Shadow Hearts Covenant) vs. Marionette Messiah (Super Robot Wars OGs) - At least it looks like the Messiah hype train goes no further. I suppose it consoles me somewhat that Messiah was undoubtedly competing against the scrubbiest pools. But Messiah is the odd one out by a lot in the final 8, to me at least.
Battle with the Four Fiends (Final Fantasy IV) vs. EXEC_SPHILIA/. (Ar Tonelico 2) - Oh, man. This one is tough. Both are extremely good with some very minor flaws. I think Battle's shortness tiebreaks against it here, as making 5 minutes interesting is hard.
Main Theme (Orchestral) (Parasite Eve) vs. Song of Mana (Legend of Mana) - Also very tough. Coinflip.
My top favorites didn't make it this far, but at least there's definitely some very strong quality left. Agree with Tonfa though, if another music tournament gets run, I'd hope that repeats that did very well in earlier tournies (say, pool champions and above; the top 16) are left out.