Well, I must congratulate you by your inovative intentions, however I think that what you pretend developing is a little bit outside my expertise. But let me try to help you if I can: You should download the anaglyph maker, or anamaker from
http://www.stereoeye.jp/software/index_e.html and try some experiments in photos or design and try to use those in your website....
Don't forget to use the adequate glasses for view the photos...