Recently I had a site with +30 000 images, they were all in default drupal folder /files and ofcourse this started to make problems for my server but also if I wanted to manually do something, delete a file or use it this made that directroy unusable. So filefield paths (which should be in core) helps here. One of the best practices so far is to have directories by dates, so each year has it's own, each month, own and day its own, but months are subfolders of years, days are subfolders of months. So to set this up add this to filefield configuration
[yyyy]/[mm]/[dd]if you have some better ideas, please write how you sort your files.