HP<->MP has theoretically amazing applicances, but none are practical so whatever. Never ever used it.

Throw, Destruct, Mystify, Transform, Time... don't think I ever used those either. Never needed Underwater either, the Emmy fight doesn't even come close to taking 20 minutes.

I might have cast Full Cure or Shield a couple of times, but ultimately went back to Restore (Regen) or Barriers. The lack of All functionality coupled with very high MP cost really hurts those materia.

I don't think I ever really made use of HP- or MP-Absorb either.

Cover is totally awesome though, especially combined with Counter Attack or on Aerith. Good old Fury Brand.