iTunes is less fussy than iPod when it comes to videos. iPod is quite specific. It accepts only two types of video, MPeg 4 & H264 which is an advanced type of MPeg 4 video. The limitations are in video dimensions & in audio specifics.
You will find more information here: How to transfer to my iPod (& iTunes) - for video. Half-way down that post you will see the specifications for video for iPod.

You may need to convert the video so it's iPod compatible in viewing dimensions & audio specifics. Video extensions would be mp4, mov, m4v ... as far as I know. There are some converters mentioned there. Do not use Anapod. I really need to update that page again. So many links die so quickly.