I know it's not Windows, so it doesn't answer your question but since we are on a maemo-forum anyway, I don't feel bad about suggesting the following.

ffmpeg, available for the N900 as well as the N9, is light, fast and extremely versatile.

In it's simplest form you would do something like this on the terminal

If you need more than that, or need better quality of reencoding, have a look at the extensive documentation, to be found here:

http://ffmpeg.org/documentation.html

Like I said, I know it's not a windows solution, but IMO ffmpeg beats anything.