Even though we've been in the house for 9 months, I'm still in the process of getting things just right in the office. The previous owner installed ugly but functional bookcases and desks. One of these days, I'll redesign it, but in the meantime, I have set up the following to be efficient:
Mail System: I have 3 baskets to help me manage the flow of papers - In, Pending, and To File. The In box is self explanatory - unopened mail goes here. The Pending box holds items that need action like bills and invitations. The "File" box is where papers that need to be filed are kept. I have successfully set up variations of this system for my clients to help them keep track of all their incoming paper work. I make a conscientious effort to go through all 3 boxes at least once a week, otherwise, I drown in paperwork.
Active Files: I have several on going projects or clients where I have to actively reference their files. I like to keep their files on top of my desk for easy access.
Frequently used office supplies
I prefer an uncluttered desk, so I keep frequently used office supplies within arms reach in drawers with dividers.
Extra office supplies/reference materials
Reference materials like magazines and paint swatches are kept in magazine files. Extra office supplies go in matching boxes. Whenever possible I try to buy matching organizers for a cleaner, streamlined look.
What I haven't showed you are other areas of the office that need work. There's a corner in the closet where I have old tax records that really should go up into the attic as I never reference them. We also have 2 printers in the office, even though we only need one. The other bookcase holds decades of old photographs stored in random shoe boxes. One of these days, I will finish the office. I sound like the old shoemaker whose children had no shoes - I'm so busy with my clients that I sometimes don't have time to do my own home!