For a number of years, I've thought about trying out a simple but (I think) interesting system for magic in a fantasy RPG (although I suppose it could be used for other genres as well). It's based on the idea that a gifted person can twist probability in his favor, but there are consequences to this action.
The basic idea is simple: the gifted character can, at any time, gain a bonus to a die roll affecting them (or any die roll, depending on how magic works in the game). The bonus can be any size (although the system you're using will obviously affect the size and meaning of the bonus). The GM keeps a running tally of the bonuses used by the character. At any time that he feels like it, the GM can then use some or all of this tally as penalties against the character. The GM can parcel out the penalties in dribs and drabs, or one huge whammy. Do whatever is dramatically appropriate.
For example, in a Fudge style game, a PC takes a +1 bonus during a battle in which he fears for his life. Later, he takes a couple of +1 bonuses to healing checks to recover from the battle. So the tally is now +3. Later in the session, the PC tries to use diplomacy to get an NPC to cooperate, and the GM drops the whammy--a -3 penalty, which leads to catastrophic failure of diplomacy.
I think this system could be adapted in many different rules systems without a problem. And it is balanced if the GM does in fact use the tally to penalize the player. I think it could be a lot of fun.