There's nothing like a new computer, a blank slate where you get a chance to start over in your digital life without all the mess - no duplicate files and no useless installers hanging around, no more scattered photos and videos and documents, no more four web browsers with four different sets of bookmarks, no extra software you never really used while the launcher continued to run in the background and suck up memory.
This time (you promise yourself), things will be different. Your computer will be clean and clutter-free, organized and logical, fast and efficient. You will be on top of things: the master of your digital domain.
But it never lasts. Sooner or later you'll have files everywhere - in Downloads, in Documents, in Libraries, in Program Files, in System Files, on your Desktop, in random folders you created to organize your stuff but that only created more clutter.
It's not always your fault, either. Chances are your computer came with a bunch of software built in, like HP MediaSmart or HP Dashboard, which is confusing. When you download software it sometimes creates folders in odd places, or duplicates your files (iTunes is famous for this).
If you can't wait until your next computer to clean up your digital life then you can always start over - back up all your really important data (photos, videos, movies, games) then insert your Mac OSX and Windows 7 disk and start over. If you don't have a disk, go to www.apple.com, www.microsoft.com or www.linux.com and do a search for the right instructions.
It will probably take a day or so to get your computer back to the pristine place it was before you put your grubby fingers all over it. Once you're there, you get to start over.
Familiarize yourself with the file structure, and create the file folders you need for your personal items. Make shortcuts if your files are buried a few menus down, and collect those shortcuts into another folder that you drop onto your Start menu (Microsoft) or Finder's "Places" list.
The rest of my advice is for PC's, but a lot of it will apply to Macs and Linux users as well.
Now that you have a blank slate you're going to need software - and you'll need to decide on a standard system for handling your software, like ensuring that all installers go to Downloads, all programs go into Program Files, and all extras - e.g. your iTunes Music folder, project folders - should go to the spaces you've already designated in your file structure. Don't be shy using the Libraries tool (right click on folders and files) as another way to track your stuff.