Recs.
Updated
Hazel is a tools for sorting files and folders. For alternatives, see here.
Hazel is a System Preference pane that works silently in the background, automatically doing basically whatever you want with the files/folders you specify. It has really useful filters for deciding which items to act on and a lot of options what to do with those items. Move them, rename them, open an Applescript, etc.
Specs
Pros
Pro Automatically cleans up and maintains folders
Hazel watches whatever folders you tell it to, automatically organizing your files according to the rules you create. Have Hazel move files around based on name, date, type, what site/email address it came from (Safari and Mail only) and much more. Automatically put your music in your Music folder, movies in Movies. Keep your downloads off the desktop and put them where they are supposed to be.
Cons
Con Rules creation is a time consuming process
To really enjoy the power of Hazel, you will need to progressively create more and more rules to manage each specific kind of file, but this process is slow, quite annoying when you have many similar rules, and can only be learned on the way, as you find new uses for it.