So I bought bourne legacy a while ago, and now I am trying to put it on my 4th gen iPod. When I do so, it says that it doesn't work. However when I try to convert the file through iTunes, it has all of the converting options disabled.
Assuming there is no DRM (copy protection) on the file probably one of the best conversion tools and the one I use is called Handbrake:
This joy will trans-code almost any video file format to almost any other video file format. It is free, easy to use and should solve your problem.
Just reveal your movie file in the Finder (so you know WHERE it is) and point handbrake to that file. Then just select the output device you want and Bob's Your Uncle!