I have all my photographs sorted into folders by year >> year_month >> year_month_day using the photograph's EXIFs information.
Currently, I've been using the Nikon Transfer program that came w/ my D90 and then sort all the transferred images into their appropriate folders.
Nikon Transfer works well with the D90, Sony Cybershot, Kodak ZX3, but not my Droid, Transformer, or DInc. A really cool feature is the fact that the program only transfers the new images on the camera even if you kept the images from the last transfer.
Does anyone know of a good software that can do both of the above as you transfer files from you picture taking device?