After a while you realize that the more time you spend just getting those pics onto your computer, the less time you actually want to spend enhancing or even just enjoying what you have produced. Workflow is such a personal issue and one which seems to get everyone a little hot under the collar, I have developed a simple process which works for me and uses mostly software I have gotten with my cameras.
Transfer files using picture project- The window comes up automatically why not use it? I choose to delete all files once downloaded, rotate automatically and synchronize date with my computer. I also chose to put the files in a new folder for every download. One thing I have also started to do lately is add pics to a collection- this helps me find them quickly.
Basic edit in picture project- I can hear you screaming from here, why not use it? I like the features, especially the lighting and contrast sliders also the color boost is great as well. I tend to shoot black and white on the camera in the case of the D200 but you can use Project to convert for you.
Advanced edit in Capture- I select hero photos and sharpen, adjust, correct and general fiddle with in Nikon Capture. Its is the best NEF conversion software around (so it should be) and essential if you shoot NEF files like me. You can batch convert multiple files and plug your camera in to upload custom curves.
Archiving- This is where I step away from the Nikon software and head into Fotostation. I add basic info such as-
Caption (keep it short and sweet)
Everything can then be transferred into my archive which is held on my firewire Maxtor external. The main point, in fact the most important thing to remember is ALWAYS CAPTION BEFORE YOU SEND YOUR FILES TO YOUR ARCHIVE, if you cant find them again they are of no use to you. Imagine a year later, you remember that great shot you did of uncle Bobs birthday but how do you retrieve it amongst the thirty thousand other pics you have sitting in that folder marked "My Pictures"?
that's about it, I also add keywords such as "favorite" or "print" just so I can find this quickly, the history function in fotostation will tell you if and when you printed something. Lately I have begun to assign things to projects which helps as well.