My hardware set-up is that I have a dedicate file server with a few terabytes of hard drives on which my photos sit.
My folder hierarchy is: -
"Photos" under which all the pictures will reside; under this are two sub-folder: -
"Master" where all the Originals will reside.
"Projects" where any cropped, framed, adjusted picture will reside.
Under "Master"
"2004" / "2005" / ... "2009" for each year
then "Jan.", "Feb." ... "Dec." for each year
then "1st --- Botanical Garden" (date, then three dashes, then the event / place) .. each day's shootings go into one folder with the folder name indicating where that place was and what date it was. The photos in that folder would be renamed to indicate the name of the event / location. In the event the day has two main events, then each gets its own folder. So, I may end up with two folders for the same date in the same month.
All pictures stored in "Master" are the RAW / NEF pictures, unaltered in any way what so ever.
"Projects and Themes" are whatever grouped of pictures that I've decided to give away, show, etc.
"Macro flowers"
"Macro abstract"
"flowers"
"scenery .. sea"
"scenery .. countryside"
"scenery .. cityscape"
"weddings"
"portraits"
etc.
Only a small handful of shots that I take make it to this part of my workflow (I shoot a few thousand shots per year, but only a few hundred make it this far).
Under each of these categories I have two sub-folders "Copy of Master" & "Final Result" I would put a copy of the "Master" image in the "Copy of Master" folder, as indicated above, only a very few selected ones end up coming this far (I never touch my Masters).
The copy would then be called the same file name as the original one with the added "Copy of Master" to the name's end. The copy of master version would be the one from where I'd do the adjustments etc., and the final result would be filed in the "Final Result" folder, with the name being the same as that from the "Master" folder only I'd add " --- adjusted Final Result #" where # will indicate adjustment number, since there may well be multiple adjustments to a single Master shot.
Some of the Project and Themes, such as weddings and portraits have sub-folder for each individual event .. e.g. in Portraits I have a sub-folder for "Daughter", "Father", "Mother", etc. These sub-folder would then house the "Copy of Master" and "Final Result"
All, of course, are imported in to my Lightroom and I do all the adjustments from there. I am only now starting to play with borders (thanks to cowasaki and Elements).