Nvidia have confirmed that Linux will get 3D Vision support but only for Quadro GPUs for now. Linux has always been big in the scientific world, the Ubuntu Software Center even has a "Science and Engineering" applications section. It appears that the biomolecular sciences would benefit from stereo support in Linux and Quadro GPUs should suite them fine. Although there are no plans to support Geforce GPUs at this stage but i would imagine that given the right amount of demand they should have no problem introducing it since they'd have already gone down that road with the Quadros.
Ubuntu is currently pushing over 12 million users and this number will jump significantly with the release of Lucid Lynx which is a long term support version of Ubuntu and a major step in feature innovation. As was pointed out in this thread; the kind of people who use Linux are the kind of people to want to play around with gadgets like Nvidia 3D vision and i am absolutely one of them. With the popularity of Linux and specifically Ubuntu rising rapidly and the popularity of stereoscopic 3D increasing thanks to movies like Avatar; i'd say we're not too far off from the required demand.