At work, I always envied the effortlessly organized and assumed that managers preferred tidy desks, if not for themselves then certainly for their underlings, so it was a shock to discover this isn't necessarily true. "Empty desk, empty mind" a manager once told me when I asked her opinion on the matter while waiting for a meeting to start. "Cluttered desk, cluttered mind," retorted another manager at the table.
While there's something comforting about being able to keep materials out--especially if you have to leave when you're knee-deep in a project--overall I find that I feel best when I clear off my desk at the end of the day. I like the way a cleared desk invites use; it feels like a fresh start. When my desk is clear, I want to sit down at it. Not only do I find that I don't mind the few minutes that it takes to get out whatever it was I was working on, but I generally pull out less than I had put away, which makes room for new things that come up.
At home, I have two desks, parallel to one another with my chair in the middle. I try to keep the desk closest to the door completely clear, while I store a few frequently-used supplies on the top edge of my drafting table next to the window. The parallel rule acts as a kind of border between my work space and my supplies, a position that also allows me to use the rule freely without having to move stuff out of the way.
Among the supplies I keep on my desk at home: bottled ink for my fountain pens, drafting brush, and stainless ruler.