I have both Quake2 and Doom, and I *thought* in Quake you could change it to southpaw, etc.... there's also legacy and so on, but I don't know what they are, since I'm a Halo man. I've got mine set up just like Halo, with the sensitivity and all to be default, and I love it to death.
Go into the options and try southpaw.
Spike