Well, that is due to changes in the sound server, which I admit is a weak spot for old game compatibility. But it is not insurmountable - or a problem that is characteristic only to Linux.
Originally Posted by AJenbo
It is also true that WINE has some compatibility advantages - I have heard of people who use WINE instead of native windows because it is better than playing there older games. Due to the fact it is by it's nature trying to emulate certain environments, that is also understandable.
In the case of Quake III though, you would probably be better off with a source port than running it through WINE though.