Part of being comfortable and working with efficiency at your desk is in the way you've set things up. Start by clearing everything off your desktop. See how clean and pristine your desktop looks? Now you can begin the harder task of organizing your desk. Put back only those items which are strictly necessary. For instance, put back the computer and your phone.
Once that's done, take a look at the rest of the items you've removed from your desk and ask the question: "Must this item remain on my desktop?" If you don't use it on an everyday basis to assist you in your work, it's time to find a new place for the item.
Next up: deal with that unwieldy stack of papers. You've pushed it off long enough. Finish what you need to do and file them away. Throw out the candy wrappers. Get some caddies and trays to help you organize your desktop and desk drawers.
You can buy any number of styles and sizes of caddies and plastic trays at office supply stores. You should be able to find some that are just the right size for your desk drawers. With some of these dandy office aids, you should soon have all your supplies organized in a neat fashion. From now on, you'll know just where to store and retrieve all those pesky pens, thumb tacks, rubber bands, and paper clips. When you need one, you'll know where you can find one.
Stacking trays are also a boon for organizing your desk. You can use them as "in" and "out" boxes. They don't just help you know where you're holding with your paperwork and correspondence; they'll also give your desk a neater appearance and help you save on space.
You can make even more work space for yourself if you give certain office essentials their own locations. For example, get that printer/copier off of your desk. It's just taking up precious space. Buy a printer stand which will free up your valuable desk space while helping you keep your printer close by. It should also give you some extra room for storing printer paper and ink.
Still short on workspace thanks in part to a small desk? Try placing an occasional table right next to your desk. This will give you the additional workspace you need to get the job done. Make sure you choose a table that is the same height as your desk.