Let's face it, the Enemy Skill materia was just ridiculous in this game. Between Trine, Aqualung, Beta, Magic Breath, Big Guard, and White Wind, a lot of magic materia was rendered nearly obsolete fairly early in the game. True, you had to know where to learn them, but once that was done one tiny materia became a complete powerhouse. Hell, if you can manage to get Beta early from the Zolom (which is admittedly very difficult), you have your most powerful spell for a good while.
What is your favorite Enemy Skill? I think Pandora's Box is really cool, but I hate that you can't learn it earlier. Big Guard is obviously the most useful, and quickly became a mainstay for me for boss fights. White Wind is also amazingly useful, healing for a large amount of damage for all allies, though is less useful if all of your characters have low HP (I believe it heals based on the HP of the caster).