Is there an application for boosting the bass levels of all system audio?
BOOM!

It's a very simple app, costs just $9 on the Mac App Store as of this writing.

We covered this app on the Ask Different Podcast, episode 15. Nathan needed an app to apply a satisfactory EQ output to all system audio, as he's begun to use Spotify more often than iTunes, and Spotify does not have an EQ function built in.

Thus, we have BOOM! A variety of uses (gain/leveling, EQing, etc.), with a simple interface, and a low cost.