Encoding in h264 for your iPod/iPhone in Linux
From Mike A. Leonetti
I did a ton of searching for this. After tons of trying out different things I found that somebody already made a script for doing everything I already wanted. In fact, the script was even in the Gentoo Portage tree (http://www.gentoo-portage.com/media-video/h264enc) and I was able to just put it on my system directly from there.
The project is called h264enc. The name is pretty much what you'd expect it to be given what it does. The home page is http://h264enc.sourceforge.net. It will let you convert from BluRAY, DVD, and from files to mp4 files that can be uploaded to your iPod/iPhone device. I tested it on the iPhone 4 myself. There was a slight syncing issue I experienced, but it was the closest I've come so far to being able to get anything natively to run on my iPhone (movie wise).
I know we all as nerds want to find some slick and awesome mplayer or ffmpeg options. I know I did. There are tons of web sites and forum posts out there that have something that you can try. Heck, even mplayer has some on its wiki (http://wiki.multimedia.cx/index.php?title=MPlayer_FAQ). But, all I've experienced was iTunes telling me that the format wasn't supported by my device and would not be uploaded. That is, until the h264enc script set me straight.