I'm James Hague, a recovering programmer who has been designing video games since the 1980s. This is Why You Spent All that Time Learning to Program and Organizational Skills Beat Algorithmic Wizardry are good places to start.
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An Irrational Fear of Files on the Desktop
A sign of the clueless computer user has long been saving all files directly to the desktop. You can spot this from across the room, the background image peeking through a grid of icons. Well-intentioned advice of "Here, let me show you how to make a folder somewhere else," is ignored.
The thing is, it's not only okay to use the desktop as a repository for all your work, it's beautiful from an interaction design perspective.
The desktop is the file system, and it's a visual one too. Everything is right there in front of you as a sort of permanent file browser. There's no need for a "My Computer" icon, having to open an application for browsing files (i.e., Windows Key + E), or dealing with the conceptual difference between the desktop and, say, "My Documents" (something surprisingly difficult to explain to new users). It's only too bad so much time has been spent disparaging the desktop as a document storage location.
What about the mess caused a screen full of icons? That's the best part: you can see your mess. You can be disorganized regardless of where you store documents, but if you just dump everything into "My Documents" you don't have the constant in-your-face reminder to clean things up. The lesson shouldn't be not to put things on the desktop, but how to create folders for projects or for things you're no longer working on.
To be fair, there were once good arguments against storing everything on the desktop. Back when the Windows Start menu required navigating nested menus, it was easier to have desktop shortcuts for everything--most applications still create one by default. That muddled the metaphor. Was the desktop for documents or programs? Once you were able to run an app by clicking Start and typing a few letters of the name (or the OS X equivalent: Spotlight), the desktop was no longer needed as an application launcher. (And now there are more iOS-like mechanisms for this purpose in both OS X Mountain Lion and Windows 8.)
The puzzling part of all this is how a solid, easy to understand model of storing things on a computer became exactly what the knowledgeable folks--myself included--were warning against.
(If you liked this, you might enjoy User Experience Intrusions in iOS 5.)