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Self-Destruct and the Aero spells are the big ones for me. Mostly cause they are traditional Blue magic and it was a bit weird not having them. If there was a way to modify the damage equation, I would say Everyone's Grudge by the Master Tonberry. Emerald Weapons Ultimate attack would be kinda neat if a bit useless but it would be another decent incentive to fight him.
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Aero 3 for me too. I don't know why but for some reason it feels like it should be an enemy skill, but isn't.
I love the ES materia though and it's the only materia I used when I last completed the game.