Something Genixia and I have already discussed was the idea of allowing the bass and treble boost/cut to be configurable per-song (via a tag in the comment field, interpreted by proc/notify). I could see this being done for AM, FM and Aux as well.
Thing is, after removing the bass boost for FM, and adjusting the relative volume level of Aux, FM, and AM with Hijack, I find that I don't desire a different EQ setting for these things now. Nor do I want a different EQ per genre for the MP3s. As long as your system is EQ'd well, all music should sound pretty good on it. Although I could see needing to reduce bass on the Aux input for a portable CD player (since they boost bass anyway).
The only reason I want a per-song adjustment it to correct for a few poorly-mastered albums in my collection. I wouldn't use it all over the map. For example, I'd just reduce treble by 3db on The Fixx's "Shuttered Room" remaster.
I think this would be much easier to manage than a per-song EQ or a per-input EQ. Just one or two values for bass or treble boost/cut. Very simple. I'd hate to have to come up with a completely different EQ setting for each situation. Once the EQ is dialed in well, I don't think you need more than a slight adjustment of bass or treble for a given source or song.