For example, my idea for a conflict in this story is that maybe the guy can't control his powers very well. And then one day he realizes that he's been using his powers on HIMSELF, and he doesn't know which parts of his life are real and which parts are illusions he created.
Crap son. That some good stuff right thurr. Beautiful mate.
And then, (I KNOW this is backwards to how most people think it should be done), I try and think of gameplay, music, and graphics that would enhance the story.
I think that's a good way of thinking about it. I try to use metaphors to explain feelings, by associating various objects/sensations with feelings. Such as an airplane representing freedom, or jail bars representing a trapped sense of mind. A "chilly" atmosphere representing suspense, or even emotional disappointment or depression. Every element in the game represents some emotion or the other, and it's good to have a coherent sense of meaning in each of the elements that make up the game.