Welcome to Linux Questions!
You could try Transmageddon.
http://www.linuxrising.org/
I've been using it to convert .avi files to Mpeg4 for use with my Raspberry Pi/nas media set up.
If you use Ubuntu, you can install it from the repositories using the Synaptic package manager.
Seems to work pretty well but I wouldn't say I'm an expert.
Play Bonny!
