.mov is Quicktime, right? I'd start by getting hold of the Quicktime Alternate codecs - I beleive they're bundled in the Kazaa Codec Pack, but you should be able to get them seperately if you search.
As for MPEG4, do you specifically want an MP4 file, or just an MPEG4 compatible file? DivX and XviD codecs (to name a few) can be MPEG4 compatible if you encode correctly with them, but I don't really know much more about differences between them and an MP4 file.
From there, the (probably universal, though not easiest) way to go about converting video formats from one type to another under Windows is to have the DirectX SDK installed (download from MS), and use GraphEdit to build a graph of filters to open the source file, decode the audio and video streams to raw streams, re-encode them using whatever you want them encoded as, then write them to a new file.
It's not as simple as it sounds though, so you might be better off waiting for someone here to reply with a program to do specifically what you want, and not a general solution