Programs like iMacsoft iPod Video Converter were developed to help Mac users get rid of incompatibility issues between their favorite clips and iPods. This application lets you choose between various output profiles, supports batch conversion, and immediately offers you the results you need.
After you import the clips you wish to convert, the app lets you choose the preferred output format. The program also provides you with two types of output configurations, one for beginners and another for the advanced users, each with an individual group of settings which you can easily configure.
Another advantage is that you can choose individual output profiles for the imported media files. Plus, the utility immediately converts the videos to the selected output formats.
Unfortunately, the app occasionally fails to convert some file formats (in my testing if failed to convert a MOV file). Another thing I didn't like was the fact that it lacks an option to attach subtitles to movies.
With that being said, I think you can find better solutions for converting media files to formats compatible with your iPod.