I don't know what's going on. Whenever I try to watch a video that isn't flash or QuickTime based, I only see the video in red and black tones. It's really starting to annoy.
I've heard about this happening before, and the reason Quicktime doesn't do this is it has something to do with using the codecs internally, rather than having them linked to libraries externally.
You can try VLC, but I doubt it will solve all problems. A quick solution would be to reboot. I'm not sure about a final fix though.