I'd gonna start with my favorite Crystal from Final Fantasy Mystic Quest. In Mystic Quest there was only one Crystal which was being taken over by the Dark King. This one Crystal while keeping the whole world inbalance was easily taken by one force.
In Final Fantasy 2 or 4 the story was invoked by the Crystal. In the intro of the game you see a certain dark knight.
Go and steal a Crystal from a peaceful village. Turns out that someone is gathering the Crytals for an evil purpose. In FF4 there were 4 Crystal on Earth and 4 in the Underworld. In the end it seem that once again only the power of the Crystal could help good prevail over evil and defeat Zeromous.
In Final Fantasy 5 the Crystal wee also a very big part of the story. The difference in this and FF4 is that as each Crystal dissapears its essence dissapears from the world. In the intro of the game the wind stops blowing which is a sign that the Wind Crystal was taken from the shirne. As the story goes on you find out that a evil that existed in another world return to take the Crystals so that he can be revived to take over the world.