Assuming the file is named "source.avi":
ffmpeg -i source.avi -map 0:2 -map 0:1 -vcodec rawvideo -s 480x480 right.avi
ffmpeg -i source.avi -map 0:0 -map 0:1 -vcodec rawvideo -s 480x480 -vf pad=960:480:0:0:violet -y left.avi
ffmpeg -i left.avi -vf "movie=right.avi [ovl]; [in][ovl] overlay=480:0 [out]" -an -y -b 4096k done.avi
Then upload "done.avi" to youtube. View the video, click "Edit Info" => "3D Video" => "This video is already in 3D" => "Save Changes"