Unforunately Youtube update their methods all the time. The latest known guide can be found here.
Essentially, you should save the videos as Parallel MP4 files. Then download and install FFMPEG.
Finally transcode the video and add the required information using the following command:
ffmpeg -i input_file.mp4 -vcodec libx264 -x264opts \ "frame-packing=3:frame-packing-interpret=1:frame-packing-quincunx=0:frame-packing-grid=0,0,0,0" output_file.mp4
Where 'input_file.mp4' is the file you saved from 3DCombine.
Starting with 3DCombine v6.17, GPU hardware acceleration is available for certain functions. At present this is only available with nVidia GPUs.
If your nVidia GPU supports hardware video encoding it will be enabled automatically when saving compressed AVI or MP4 files. You can check for this in the about box. It will say 'hardware video compression available.'