Have a place for everything. Some suggestions might include:
have an in box for incoming things you need to sort through and review; have an out box for things you've looked at that need to be filed or sent to a different place;
label file folders in a file cabinet and file away papers immediately instead of placing them on the desk.
Keep 3-ring binders with important forms, passwords, codes, etc., that you refer to often. Make sure they are labeled and put away on a shelf for easy locating.
Don't keep a lot of unnecessary items on top of the desk such as office supplies except for things you use daily like pens and pencils.
If all else fails, every so often (like every two weeks), take everything off your desk and place it in a box. Clean your desk off and put back what you need. File away everything else where it is supposed to go.