I’m of the camp that likes to have a pristine desktop. I personally think the desktop should never be seen, and if it is then you’re not managing your windows properly. When things go on my desktop I naturally try to clean them up. I don’t need any application launchers because I use Launchy for that.
In the past I used to use a dedicated Downloads folder. What has always happened was a convoluted mess of files that I had no idea what they were or not sure if I even needed them. Since the folder was sort of out of the way I let it get messy. Since I already know I’m crazy about keeping my desktop clean I thought it would be interesting to make it my default download location. The result is that I’ve been diligent in following GTD actions with the files! If I need the file once I’m quick to delete it. If it’s important for something later I put it into a hold folder, and the last case is that I store it for reference.
This probably all sounds obvious, but reading GTD is like reading a design patterns book. Instead of everything looking like a singleton or a factory, I see things in their context, project, and next action.