Since getting my Nikon D70 I have struggled with different image editing applications to process the RAW images. For a while I was using Nikon Capture 4.1, but was never satisfied with the application due to it's many bugs, quirks, and horrible user interface. While I owned Adobe Photoshop CS, I didn't use it much for RAW editing cause I wasn't really sure about what I was doing. A few weeks ago I picked up Real World Camera Raw by Bruce Fraser. I finally finished reading it this past weekend and learned a lot. Enough to ditch Nikon Capture for Photoshop to do all my RAW editing. I also started to use the File Browser in Photoshop CS to manage my "workflow" which the book touches on. Up till now my workflow was very ad-hoc. The book is definitely a must read if you deal with RAW images. If you don't own Photoshop, all the material is directly applicable to Photoshop Elements 3 which has the same RAW support as Photoshop CS.
note: if you happen to edit any Nikon RAW images using Nikon Capture (which will save any changes to the original RAW file), and that image is in portrait mode, you will suffer an unfortunate fate. It seems that Nikon capture really mucks with the Camera EXIF data, resetting the Exif Orientation values for the data and embedded images. As such when you view the images in the Photoshop File Browser they will not be rotated and you will need to manually rotate the images. The sad side affect of this is that the rotation setting is persisted only in the Browser Cache, and not in the image itself. As of yet I have not found any work around for this issue. I consider it a bug in Nikon Capture (and I doubt they will fix). Lesson learned. Editing the original images in Nikon Capture was a bad idea.