This and mencoder is the only open source video converter I’ve come across that can, in theory, output H.264 for the ipod, in addition to a huge variety of other formats. Videolan also has some interesting possibilities. Both are a little nerdy to set up, but hey, I’m feeling nerdy.
MeWiG is a Windows Frontend to the MEncoder (part of MPlayer) using the .NET Framework. You should be able to crop, scale, deinterlace, etc and finally convert almost any digital video-source, without the need for commandline-options.