Handbrake is a great tool for encoding video. Best of all it is open source and free. If you are running Ubuntu server, here are the steps to install it quickly and painlessly!
$ sudo su
# apt-get install python-software-properties
(hit Y to continue)
# add-apt-repository ppa:stebbins/handbrake-releases
# apt-get update
# apt-get install handbrake-cli
# HandBrakeCLI -u
HandBrake 0.9.6 (2012030100) – Linux x86_64 – http://handbrake.fr
Your version of HandBrake is up to date.
Find your encode settings then start encoding, woohoo!