The D100 is a good camera, it has it's draw backs, but you will be happy with your purchase. The EXTRA $160 plus, for the Nikon Capture 3 Software is a good investment and a drop in the bucket considering the amount of money and time spend on the other lenses and accessories you have, or will purchase. You wouldn't think twice about a product, at that price, that can dramatically improve your image quality the way this software can if properly used. Nikon has been a slow starter when it comes to image capture software and it is still clunky here and there, but they are improving their applications all the time (Capture 3.5 end of November, maybe). I believe that Nikon is just beginning to take advantage of their .NEF image file format.
Do keep in mind that the software does come with an Adobe Photoshop Import plug-in. You can still do some basic things with the .NEF files and the import plug-in when used in Photoshop, like color balance and exposure variation. It does limit your options when using the Photoshop import plug-in compared to the Nikon Capture 3 software.
Now, if I could only purchase a "Buffer Service Enhancement" like the one recently announced for D-1X, for my D100. Double or triple my buffer size? YOU BET!! I would be happy to spend Nikon another $234.00, plus local tax, shipping and handling $12.50. No kidding.