Treat Your Desktop Like a Desktop
You should keep your desk at your office clean. When you come in to work, it’s nice to have a clean work area. This increases productivity. Throughout the day, your desk won't stay clean, though; you will have papers everywhere, sticky notes, food, drinks, and so on. However, when you leave for the day you should clean your desk up and file your papers in corresponding folders and drawers.
The same should be done with your computer desktop. Would you leave a document that you haven't used in months on your office desk? No. So why would you do that on your computer? If you treat your computer how you would a physical office workspace, organization will come naturally.
Also, keeping files on your desktop slows down your computer. Your Mac shows what’s in each file by showing a thumbnail preview. This is a great feature. If you have pictures, for example, you can tell what each one is without opening up every file. However, showing you what’s inside all of your files uses up your computer's memory (RAM). There is no reason to be using your computer's RAM on files you haven't opened in months.
Lets go through the default locations the Mac Operating System gives us to store our files. If you do not have a Mac, the same logic can, and should be, applied to your own computer.
Your work space. Where you store the files you are working on throughout your day.
A customizable place for you to access the apps that you use often. The dock remains (by default) visible all of the time. Think of the dock as something on you would always keep out on your desk, such as pens, paper clips, a stapler, a phone, calculator, etc. There are many applications that you use too frequently, that you shouldn’t hide away.
There are many applications that you don’t use everyday, or every week, or even every month, but you still need to keep on your Mac. This is where you store those apps. You probably use Safari and Mail everyday, but do you use iBooks everyday? If not, it shouldn’t be cluttering up your dock.
Have you ever thrown a document away at work? Ever shred a picture of your ex girlfriend/boyfriend? Now you can do that on your computer too!
Think of this as your filing cabinet. Inside the app Finder you have folders called Documents, Downloads, Pictures, Movies, and Music.
In Finder, you can make subfolders for each of these so you can organize them further. For example, you can have a subfolder called School in your Documents folder, then another subfolder called English 101, and then another subfolder in that one called Papers. This type of organization is called nested folders.
So now if you need to find your english essay that you wrote three years ago you know that your essays are kept in Documents > School > English 101 > Papers. This is far easier than searching your entire computer for one file. This same method can be used for pictures, music, movies, and so on.
I personally have three main subfolders in Documents; Personal, Work, and School. Then under these folders I have many more nested. Everything I do can be categorized in those three subfolders. This is my preferred method of organization; you can customize this to fit your needs better. You may need many more categories, or you may want to use different titles.