A Google employee has a working prototype of what 3D videos would look like on YouTube.
"YouTubePete" said in a YouTube forum thread that he's the developer working on making a stereoscopic player during his "20 percent time" at Google.
The sample video, which was dug up by SearchEngineRoundtable.com, can be found here. I happened to have a pair of amber/blue glasses lying around, and when I finally found the correct mode in the drop down menu to the bottom right of the player, I did indeed see 3D. It was grainy and dark, but it worked.
Pete reiterates that it is just a side project and doesn't seem to be on the agenda for the company. But he is taking feedback if you have suggestions.