I've used VirtualDub to compress video to divx format, but then you'll end up with an avi not an mov. You may be able to create mov with it as well if you have the right codecs installed, I'm not 100% sure. VirtualDubMod is a popular modified version that adds a few features, it may be worth checking that out as well.
In general, I would recommend checking out
www.doom9.org. You can find a wealth of information there about video encoding in the Guides section and lots of links to good, free software in the Software section.