I have them organized in Aperture according to date, going back to 2001.
When I "Show Package Contents" and look in the "Masters" folder, it shows four folders: 2011, 2012, 2013, and Capture.
Unless I'm mistaken, all my photos, now that they're "Managed", are in the "Masters" folder somwhere, but where are the years 2001-2010? I would have expected them to be in the "Masters" folder, but they're not.
The "Masters" folder is organized by date, but not by the "Capture" date, but by the date of the import session. If you import an image that has been taken in 2001 now, it will be filed in the subfolder 2013, not in the 2001 folder.