I hope your third paragraph is a troll post. Who cares about low-level sound? OpenAL, SDL_mixer etc. do it for you. OpenGL has awesome support for older hardware and software, don't know where your problem is with that. I don't want to start a flamewar here, so I'll just say that Direct 3D can not be regarded as superior. Anyways, that argument is pointless because there's Steam for Mac and Mac has pretty much the same gaming related APIs Linux does. The rest of your argument is kind of true: The diversity of Linux is flabbergasting and it might not pay off because most gamers have Windows anyways. But come on, are the best games those that "pay off"? If that's what you're after then it's FarmVille and stupid puzzle games, Steam games have quality.
The Trauma Center series is probably the most medical computer game I know. It's still rather anti-educational though.
Highly paid researchers torture mice for a living. It's kind of sad.