There are several video/audio encoders available in Linux like Ffmpeg and Mencoder. But not everyone like the commandline version very much. But there are also GUI front-ends for both these encoders. Avidemux and Vive are the GUI front-ends for Ffmpeg. And GMencoder is the GUI frontend for Mencoder. I built a deb package for these to install them on Ubuntu.
In order to use these tool you must install the Ffmpeg/Mencoder through Synaptic.
Also if you don’t want the GUI’s and stick with the commandline version. This page helps you to create custom commandline arguements for Mencoder.