If you are using Debian Wheezy, you can directly use repositories. I tried compiling HandBrake, but it requires many dependencies, which is a pain to resolve sometimes.
http://handbrake.fr/
Simply add this line to your sources list and update.
deb http://www.deb-multimedia.org wheezy main non-free
Then run, apt-get update && apt-get install handbrake handbrake-gtk
Note: In version 0.9.9, wmv video conversion is not available.