There are many video converter software which turn various video format to mp4. I was using MediaCoder before, but I prefer handbrake. Handbrake is much simple and easier. (A quick tutorial was shown at the later part of this post)
A common problem with convert iPhone (iPod or iPad) video is, only specific parameter setting (eg. video resolution) will be accepted by i-devices. Sometimes we converted a mp4 (or m4v) file, but it just rejected by the device. We have to put the specific parameter, especially the display resolution and audio format. Is difficult for normal user like us to get the right parameter for the i-devices.
Handbrake is an open-source software which convert mp4 file, it makes the job so much easier. Handbrake is available on Windows, Linux and Mac OS X. If you ignored the subtitle, multiple audio track and other advance features. Convert iPhone video is just as easy as one click operation with handbrake software.
Handbrake came with some preset profile like iPod, iPhone. The handbrake version 0.9.5 support iPad profile too. Handbrake convert variety of video format, but I always have problem to convert rmvb (real video to mp4) with handbrake. For real video, I suggest to try MediaCoder, another open-source video converter, it has specific iPod (iPhone) preset profile version.
A quick tutorial for handbrake.
When you first launch handbrake, it will ask for the source file. Or you can click on the source file icon on the upper left corner of the software.
Choose the iPod, iPhone or iPad profile listed on the right.
Click start and then wait, that's it. It could take some time to convert the video file, it depends on the machine speed, size of source file, size of target file. It may takes 15 minutes to more than 1 hour time.
This is just a short and simple tutorial to convert mp4 video, hope I can share more next time.