*** Boom - may be not bad App, but their EQ is not (in my opinion) good
*** Hear (by JoeSoft) - may be better than Boom since it has mush more option some of which doesn't work properly (such as EQ, when its resolution is set to more than 32 octaves it start to distort sound)
*** Apples AU lab - I think is the best option. Install Soundflower than download AU Lab, unzip, open DMG and copy to Applications "AU Lab", than open "Correction.trak" by it. You may need Xcode to download (but I am not sure). One good thing about AU Lab is that you can use not just 1 EQ, but also compressors and others VST plugins and audio units. Also check out http://www.dctrwatson.com/2011/06/os-x-system-equalizer/
I am using the last method right now and it works nice (OS X Lion). Bad side of it that AU Lab needs to be always enabled and it is not 64bit.