One of the oft-annoying issues with Drupal is file handling. There are many problems with Drupal's file handling at present (fortunately there's considerable effort now to improve matters for Drupal 7 that looks very promising), but today I just want to talk about a seemingly simple problem: Where to put the files directory. It's not as simple a question as you would expect.

http://www.palantir.net/blog/files-and-multi-site-and-migration-oh-my