MoviesForMyiPod is easier to use than QuickTime Player Pro since it is single purpose, but also it's more easily powerful for this singular purpose because it gives you simple quality options, including the option for MPEG4. QuickTime Player Pro doesn't put that option out in front when it comes to converting videos for the iPod and while you can do it with QP Pro, you have to know what settings to select. With Movies For My iPod it's a simple and quick pop-up menu selection. Also the watched folder option is great for automating the conversion of downloaded videos.
MFMiP also offers a queue, however I found it either confusing, or impossible to remove items from the queue or re-arrange them, and the queue is represented textually. The queue needs work. Also the program doesn't support drag and drop - you can't drag a video onto its icon in the dock to open it.
A feature I'd like to see added is the ability to add custom settings as menu items in the pop-up menu. Also, I'd like the option of having it automatically add the converted videos to iTunes. If that is added, it would be even nicer if it automatically placed the converted videos properly into the iTunes hierarchy of folders so that iTunes didn't need to copy it and you don't end up with two copies of every converted video. Alternatively just offer the option to move the video to the trash after it is added to iTunes.
When it comes to putting video on your iPod, this program offers more features than QuickTime Player Pro, is easier to use and is free. What's not to like?