An article on Shugashack has news that when Quake III Arena becomes available, the Linux version will be sold in stores as a separate release, rather than the way previous Linux Quake/Quake II releases were handled, which were free, but required buying the DOS/Windows versions of the games. The article offers an interview with Zoid on hardware support and other Linux Q3A issues. Here's a quote from John Carmack on the subject:

All ports so far have been just for the heck of it, but we will be rolling out real commercial linux versions of several products in the next couple months. I think the market is good enough to make real money in now.

The linux boxes will definitely be on some store shelves. Places that have existing linux OS packages will probably have the game boxes.