When your desk is messy, you just can't get work done. Important documents and things can become lost. Organizing your desk is a great way to be able to use your desk to its fullest potential and you'll certainly be able to get more work done.
Organizing your desk is actually very simple and will make your daily routine at it go a whole lot smoother. If you have any drawers that are directly in front of you use them to house items that you don't need on a regular basis, as you already know it is much easier to grab something in a drawer that is just to the left or right of you than in the drawer that is directly in front of you. Deep drawers should be reserved for obviously items that can not fit in the shallow drawers and the upper drawer to your right or left should be reserved for pens, paperclips, staplers and other items that are small but used on a daily basis.
As far as the top of your desk goes save this space mostly for free space, where binders can comfortably be opened and of course where your computer can be stored, assuming that your desk will have a computer on it. Ideally having the tower of a desktop computer off the desk is good as this will give you more room. For sorting paperwork and mail have a paper organizer at the back corner of your desk, center your computer or at least the keyboard with your chair and use a small pencil cup to hold pens and markers if those are something that you use on a regular basis. If you want to have more than just pens, pencils on the desk at all times, rather than using several little organizers, for notepads, stapler, tact's, etc., use a desk organizer.
Desk Organizers - having a desk organizer can help you keep all the little things that you want to use on a daily basis out of the drawer and on top of desk at easy reach with out cluttering your desk up.
Paper Organizers - with all of the mail to go though and paper work you do at your desk having a paper organizer can help you keep your desk nice and neat, as well as keep track of everything.
Keep your phone on the side of you with the hand that will answer it and make sure that it is close enough that you will only have to lean forward, and not get up, to answer it. As a safety precaution avoid putting precious nick knacks and picture frames on your desk, as they can easy get knocked over and break. Instead display them proudly on a shelf above and behind or beside your desk.
To ensure that your desk stays both organized and functional, at the end of the day take a few minutes to straighten anything up. You may also group together documents or notes of what you need to deal with the next day and place them in a folder sitting on top of your paper organizer. This way when the new day starts you will not waste anytime gathering what you need to start the day's current project.