I usually hate linking to WebUpd8.com because their posts (like too many Ubuntu user blogs out there) are usually too fast to tell you to add random PPAs and unknown packages but in this case, they have the best information.
PulseAudio (the sound backend for Ubuntu) supports a system-wide equaliser as of Lucid. It doesn't provide one but it has the nuts and bolts to let one transform the audio that passes through PA.
This application was written and released on UbuntuForums but as it doesn't work for Maverick (due to a broken icon of all things) there's a package built by WebUpd8 that addresses this:
I wouldn't add their PPA. Not because I think they're somehow evil but because it'll probably move you to versions of software that we can't support here. Just download the single deb and double click it.