The same way I organized my negatives and transparencies: chronologically. One folder for each year, then sub folders for each assignment. The sub folders have the shoot date as the first 4 characters, then a short one or two word description, so if I were shooting a portrait of Joe Sixpack this afternoon, the folder would be
0728 joe sixpack
and that folder would contain all the raw files from the shoot. Well, the ones I end up keeping, anyway.
All raw files are renamed using the shoot date in YYYYMMDD format, then a very brief description, then the 4-digit frame number generated by the camera. So Joe's portraits would be named:
where 1234 is the frame number.
At work all my photos get a complete AP-style cation, along with plenty of keywords that make them searchable by various colleagues who need photos (designers, web content editors, etc.) At home I use a similar organizational system, but sadly I don't often add captions or keywords to the photos. At work, the raw files are converted to JPEGs using Lightroom 4.1, then uploaded to an online web-based DAM service to which my colleagues have controlled access.
Is this what you were asking?