I agree that Materia is probably the most versatile magic system. I didn't really take the time to master, it though (my most impressive combo was Cure<->All Hahaha!). But I have seen some pretty awesome materia combinations.

I really liked Junction as well, and it was pretty fun to use.

My favorite probably goes to either FFX's sphere grid or FFX-2's Dressphere. Though probably not the most 'powerful' I found them very fun to use and gaining new abilities didn't seem like a chore.