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In case you don't know, FFmpeg is a command line tool for encoding and converting a numerous video and audio formats. x264 is a free software library (also command line) for encoding video streams into the H.264/MPEG-4 AVC format.

FFmpeg and x264 in the Ubuntu repository does not support some encoders, formats, and codecs (which are restricted).

There is a quick way of enabling the restricted encoders but it will not work for all of them. In Ubuntu Karmic, run the following command in a terminal:
sudo apt-get install ffmpeg libavcodec-extra-52

For Karmic, the libfaac codec has been disabled in the "extra" (formerly known as unstripped) libraries because it is considered non-free. The only way to get it is to compile ffmpeg yourself.

FakeOutdoorsman @ ubuntu forums has posted a great tutorial for compiling the ffmpeg and x264 yourself for Ubuntu Karmic, Jaunty and Intrepid. You can find this great how-to, HERE.

After enabling the restricted formats, you can use these additional resources for using FFmpeg: