The Nikonscan 3.1 software (make sure you get the latest patches off of the net) is excellent. Run it as a standalone, rather than a plug-in through another program like Photoshop. I turn on ICE to "Normal", which cleans up the odd bit of dirt or hair, and otherwise don't do anything to it in that program, except save it at excellent quality, normally at about 3000 pixels wide.
For other programs, I use ThumbsPlus and Corel Photopaint 10. ThumbsPlus is used for cropping and color saturation modifications, and Corel is used for resizing, color balance and sharpening.
The only thing you should feel when shooting a terrorist: Recoil.