Sadly they aren't games, but the coolest magic systems I know are in The Kingkiller Chronicles and Mistborn books.
The first has two systems. The first, the most common one, is sympathy, a kind of energy manipulation. It's a mix of alchemy and physics and is mostly used in artificing. It works by creating links between objects, the more similar the objects the better the link and the less energy is lost when applying energy to one of the objects. For instance, a link between two halves of the same stick of butter is really good. When you then apply heat to one half, the other half melts almost just as easily. However, when you link a stick of butter and a twig, and you set the twig on fire, the stick of butter barely heats as the two objects are so dissimilar.
What makes it so awesome is that this gives you untold possibilities on how you want to apply it. It's a really basic system; all it entails is creating links and degrees of energy conservation. Links can also be set with certain runes, which is called sygaldry. And with that the sky's your limit.
There's also Naming, which is more traditional magic but a lot more primal and rough. You can call the true Name of the wind (title drop of the first book) for instance which then either whips up a gale or pushes a small amount of air in a choking person. It's often very unconcious and extremely rare, and a lot of people in the books either call it strange demonic nonsense or doubt it exists altogether. People using sympathy aren't much trusted either.
Magic in Mistborn works by ingesting and 'burning' metals, with each metal giving a different power. For instance, ingesting and burning steel gives you the ability to push against other metals. This too is quite rare, with most people who can only being able to burn one metal. Extremely rare are people who can burn all of them, and then the awesome synergy between metals comes out. It also helps that Newton's Third Law is also a thing; a person pushing a coin shoots the coin away, but the same person pushing against a metal roof pushing themselves away. So you get these awesome Magneto-esque battles, but actually better because they're still governed by physics.
Metal burning could work in a videogame, I'd say, and Sympathy and Sygaldry would be just the best in a tabletop RPG.