Organizing WP-Content Folder

So I have 250,000 files in my wp-content folder. I can no longer do auto updates because php times out before it can load everything. I understand that there is a way to organize this folder into months or something like that, is this something you can do after you have this many files? We started running the site (stupidcelebrities.net) in 2006, I don’t think this option was available then, at least I didnt see it.

Any help would be great, I am in desperate need of reorganizing!

Thanks,
Jeff