Well, I made Hockey themes skins once, I actually made two, Montreal and Toronto. I origianlly made it for fun and thought nothing of it, then I was receiving tons of emails from people who wanted me to do their team. OK, I thought, it would be a cool project to make all the teams of the NHL. But with such a big project, I thought, I better make sure it'll legal. I don't want to spend a few months making somthing that I'll have to pull in the end. So I emailed the NHL about the legallity of using the teams logos. Well, I did get an answer, it took about 10 days. The answer was quite simple: for free or not, for whatever use, it was a big no no. The email explained to me what a trademark was and blablabla. Of course I knew the team logos were trademarks, but i really didn't think they woud care since it was for free. Anyway, apparently they did mind.
So, I would think your problem may be somewhat similar. If you are using the actual Quake logo, it's probably a big no no (trademark), if you are using graphics from the game, then it's not trademarked anymore but copywrited... and it's proabably just as bad.
So, overall, I would say, if you want to be legal, don't do it unless you get an explicit OK from the game company...
