Not all messy folders are alike: The stuff in your Temp folder differs considerably from the stuff in your Downloads folder. But one system is uniquely disorganized--at least on my system--because it's not all my clutter: Dropbox. Once you start sharing Dropbox folders with other people, the folders quickly become unmanageably messy: You, Jane, and John share a folder, and files quickly start popping up. No one wants to delete anything, in case another user may still need one of the seemingly superfluous files. SortMyBox is a free online tool that might be able to help, though it requires some discipline to use.
To use SortMyBox, you have to go to its website and permit full, unconditional access to all of your Dropbox files. If that idea makes you uncomfortable, you aren't alone: I feel the same way. One reassuring fact is that SortMyBox is open source, so anyone who can understand the code can audit it. Once you let SortMyBox into your Dropbox, it will set up a SortMyBox folder at the root of Dropbox. You can then configure rules that will apply to any file that pops into that folder, much as you can with RoboBasket or DropIt on your local machine. Once someone places a file into that folder, the app will sort it accordingly. SortMyBox will take files only from that folder, but it can plant them anywhere else in your Dropbox.
To use SortMyBox effectively in a team setting, everyone involved must place new files into SortMyBox; and doing so requires disciplined users and (as with all such systems) accurate filters. But if you satisfy these two simple requirements, SortMyBox might be able to help you organize your messy Dropbox.
Command-line utility SDelete securely removes files
Sometimes, you don't want to sort your files carefully; you just want to delete them, and be sure that they really are gone for good. At such times, the simplest, most bare-bones options is SDelete, a free command-line utility from Microsoft's Windows Sysinternals.
You can use this 81KB download to delete specific files, or you can have it wipe all free space on your hard drive to securely remove all traces of old files. After running it with the -c ("Clean free space") option, your drive should be virtually impervious to attempts to recover deleted files (as long as they're not sitting in the Recycle Bin awaiting easy retrieval, of course). When properly set up, SDelete works well as a scheduled task, periodically cleaning your drive; but because the utility is so minimal, you'll have to set up the task manually, using the Task Scheduler built into Windows.
Eraser scrubs data until it's gone