This is a serious pain. Your iPod may not play videos formatted for your PC. You need a special program to play Flash videos.
The number incompatible combinations is mind numbing.
Quick Media Converter has a simple interface and can handle almost any format you throw at it.
Just click a picture and point to a file and it converts it to the compatible format.

Check it out on PCWorld's website. Converting media files to another format just became much easier!