I would suggest that you start by reading over a lot of the old posts in the remastering forum, and there is also a Knoppix remastering section in the wiki (documentation link near the top of the page). I'm not at all clear that this is a very wise or useful move though. Quake III loads a lot of info from the pk3 files both when it starts and when a new maps starts. A slow device here like a DVD drive will have a big impact on game play (I would expect that by the time you get into the game other players would already have several kills). Also Quake wants to be able to modify the config file and perhaps other files (at the least a games.log file). And the Q3key file seems to be writen to even though the key never changes (looks at the last modified date on your Q3key file).

I'm a big Q3 fan, but this doesn't seem the most partical thing to attempt. At the very least I would suggest copying your entire Quake III Arena and baseq3 files to a read only media like a DVD and trying to run quake from there. If you can't run it and get acceptable performance that way then it doesn't seem like you are likely to do any better putting the OS and Quake III on a live DVD (which will be a larger resource drain on the system). Easy to determine if the concept is viable before getting into a complete remaster.

If it does work, or even playing Quake from a baseq3 saved on DVD works, please let us know.