I've just been trying that with my Trackmania glasses. It works pretty well considering the simple device, the HUD really stands out against the background... but those eye cancer colours, oh my
How did you create the stereoscopic video?
Hehehe, I just recently installed that driver and bought some anaglyph glasses for 2,50$ on dealextreme. Haven't tried Aquanox yet, but playing N64 games in anaglyph 3d is great.
see this page for a pretty good comparison.
From my experience, half-colour anaglyph works best. You'll lose most of the red colour information, but it causes the least strain on the eyes and doesn't change the original color setting too much. It's tricky to set up, though