If you don’t know about Ubuntu it is time you learned about this great free Operating System for your computer. In the mean time if you have Ubuntu or are considering installing it, then you will love this free app SYSTEM-WIDE PULSEAUDIO EQUALIZER.
It is not currently being updated and it was last released for Ubuntu version Lucid Lynx however, it seems to work fine on 12.04. I installed it today and found it great for configuring the sound of my speaker system.
Give it a try by following the instructions here: http://www.webupd8.org/2011/04/system-wide-pulseaudio-equalizer.html