I found a great app for Linux and Windows to do the capturing called wxAstroCapture:
http://arnholm.org/astro/software/wxAstroCapture/
I tried MEncoder at first, but it's a bit too generic, so it didn't have controls for the shutter speed, etc. wxAstroCapture did a great job, though. I also found ImageJ, a medical image application that can register (with the StackReg plugin) and stack the images. To export the videos from wxAstroCapture as images to import in to ImageJ, I used transcode.