Thanks for all the suggestions! Ripbot didn't quite work, I must not have had it on the right settings, but virtualdubmod worked like a charm. The filesize is down to 31MB which is way better. The playback is very smooth now. There's still one place in the video where it's discontinuous, and things seem to suddenly jump forward, but I can live with that. Probably a glitch due to the computer doing the recording needing so much processing power to store such a volume of information.

David, I tried the playback in mpc as well as regular Windows Media Player to begin with and both had trouble with the file when it was huge. Ordinarily, I'd love to supply you guys with the file to play around with, but at the moment this is unpublished research data, so I can't really circulate it in case my supervisor wants to publish it in a journal. Maybe I can take another video with the microscope camera and see if it has any discontinuous points in the recording. I'll let you know if I have a file for you to look at.