I use DVD Shrink to rip my DVD's and then Handbrake to convert them to ipod compatible MP4. Then I open iTunes, click Video, and then open the location I have for the file, and drag and drop. (Using Windows, btw)
From some of the posts I have read on here, it seems that MP4 video, doesn't always mean COMPATIBLE video.
My best advice is to go download handbrake(FREE!) and use it to make sure that your video file is compatible with ipod/iPhone.
Sometimes that happens even if you click "Add file to library" from "File" on the top left corner of iTunes. Try to use a different converter for the mp4's that didn't show up on iTunes. It usually works for me.
Apple is a bizarre company they complicate things. I had the same issue here and figured out the problem. What you have to do on iTunes is click File then Add Folder then it will import all movies in that folder that it recognizes. I tried the drag and drop the mp4 option but didn't work however this add folder worked and it imported everything.
I've done some MP4 transfer before and iTunes have no problem importing those videos.So maybe your iTunes version is not the latest?Or maybe you should just get a professional transfer program like they said above.