Heh, that would be pretty neat to try, a red-blue 3d windowblind. The problem is getting all your other apps to look ok at the same time.
Actually, a while back I spent some time experimenting with a different method of desktop depth illusion, but didn't make a lot of progress. What I tried was a mouse cursor that was actually two slightly different images side by side. Then I would focus on the cursor using the cross-eye method (familiar to stereogram viewers). Of course, the rest of the desktop was then an unfocused mess, and if you focused on it, you lost the cursor illusion. This approach doesn't seem feasible on full monitors, but small phone or PDA screens might really work.
Then there are polarizing glasses, and new flicker methods, which I know less about, but I think they'd have more potential for a full 3d computing experience as the wouldn't suffer from the color distortion of red-blue glasses, and the effect could possibly be applied to the entire screen at once, rather than one part (like with a 3D windowblind, your window edges may be 3d, but what about icons, and window content, etc.)
I think you should try making a skin, maybe not a full windowblind (skin a widget, or make a few icons maybe), in the analglyph 3D. Then show us!