I've unfortunately got no personal experience running 3D through my computer, nor with the GoPro2 yet, but what I do know is that for "proper" 3D, you need a 3D-capable video card (most of the newer nVidia/ATI cards I think?) and monitor. Unless things have changed, generally the monitor has to be/support 120Hz if I remember correctly.
Generally the 3D glasses will come with your video card and/or may be purchased separately.
Take this with a grain of salt, as I'm going on what my friend's computer setup was and that was a year or so ago.
I'm wondering if your GoPro setup is right though, not sure if it should be displaying the side-by-side video like that. Running both GoPro2's, and newest firmware?