Here are just a few ideas:
Get some of those Serilite boxes that have 3 trays in them to put on top of your desk (they are stackable if you need more trays).
I would also suggest different file drawers for each of your seprate activities. Use manilla files for everything, and organize w/ hanging files. At the end of the year I make new manilla files, and put last years stuff in one of those white storage boxes to keep on file.
A cork board is a great idea. Mark off 3 distinct areas, make them different colors, or divide w/ ribbon, ect. so that you can post important things where you can clearly see them at a glance.
I really like having enough of everything in my office. Right now I need to get a new 3 drawer file cabinet, and a nice book case so that I can get to things better. Right now I have a bunch of stuff in the closet, and that makes it harder to get to it. I also need to decorate in here. I think if I made the place look homier I would enjoy it better. I really like my desk, though! I have an l-shaped desk, so that I can have 2 different work places if I need to
I'm looking forward to hearing some other great organizational ideas!!!