The Enemy Skill materia is definitely a powerhouse item, even more so if you use the extra copies. I'm trying a run-through where most magic (green) materia is disallowed, as are summons. So my only way to use damage-dealing spells is through E-Skill. We'll see how that goes.

As for my favorite one, I liked Aqualung and Trine because they look cool. The one unfortunate thing about E-Skill is that some of them are just plain stupid and/or irrelevant after a time. Examples: Matra Magic, L4 Suicide, Chocobuckle.