I'm no expert either but I'll attempt to answer some of that.
Games like Quake 3 more or less are just cranked out in C++. It's a bit more complicated than that though. So far as I can work out, basically the game engine is programmed to represent 3D objects like players and walls and items and stuff. I think the game engine itself uses some kind of script system (like a batch file) to build a level with items in it. How the 3D graphics are linked in I am totally unsure about.
Actually I'd be fascinated to hear what other, more knowledgeable, people have to say on the subject.
