The implementation of the universal 3D video player on Youtube was the work of Google’s Peter Bradshaw, who thought of the idea of combining left and right images in to multiple 3D formats, right in the player. He built it in about 3 weeks time. That was then: How YouTube 3D Came to Be.
For reasons unknown, as of September 30 2014, the user interface for the 3D video options has been removed by Youtube. No explanation has been given. 3D options still remain in the Advanced Settings pane of the video upload page. Perhaps the 3D player options will come back?