I'm still in the experimenting stages and haven't settled on anything yet. Astrostack doesn't handle 640*480 very well for some reason. Part of it is its 32meg use limitation. But I think the sharpening and deconvolution are optimized for lower resolutions.
For just about all my ToUcam images on this site, I've been using AVI2BMP. It has alot of nice selection/deselection and save to BMP features when reading in AVIs. It isn't very flexible, but it gets the job done and well.
I've been experimenting with Iris as suggested by someone who e-mailed me. It's very powerful and very complex. If anyone can point me to some straightforward step-by-step examples other than the ones from Iris itself, please drop me a line.
I'll post more here as I narrow into a methodology I'm comfortable with. I'll probably be playing with my 2/19 Jupiter pics as a test case for a while.