I've read the Mugen ECU is makes a big difference over stock. I think it helps with the low end alot. However, it isn't programmable and is "for race use only," so it voids the warranty. Spoon makes a racing ECU also, but I'm not sure if it's programmable. They both run about the same price ($1,000+). I think AEM has one for the S2K also, not sure though . . . but it could be considerably less and would probably be programmable.
Another route you might want to consider is a VAF-C. They are considerably less and if properly tuned, they yield some good power gains. Also, there's the new Greddy E-Management system, which does the same thing with the a/f ratios that ECUs and VAF-Cs do . . .