Acoustical treatment is better than any electronic adjustment you can make. Just taming some of your first reflections could improve your sound dramatically. If you're taking such an approach, don't forget about treatment on the ceiling as well. Also, if you're afraid of putting up acoustical treatments because of the way they look, you should look around before making that decision. Since the home theater boom, many acoustics companies are now producing products that blend into a room much better than you would expect. Start with the Auralex acoustics website and work from there...

If you set on using electronic methods, you could look into an outboard equalizer to insert into your system. Here's an article you may be interested in:

http://www.enjoythemusic.com/magazine/equipment/0705/behringerultracurve2496.htm