When I remodeled my home office, I kept a photo journal and wrote a photo essay about it for WOW-Women on Writing magazine. Looking back at those photos pushed me to write a little about my freelance office organization, in the hopes it might offer some insight to others.
Desk: My desk consists of a laptop, a calendar, a cork board, and a "Current Projects" folder. I'll go into my computer records arrangement in a moment. SO, let's look at my calendar. I use a large desk calendar that's immediately to my right, and also works as a mouse pad (I'm sort of a minimalist, I can't stand to have too much clutter on my desk). This calendar notes the basics: when pieces are due, when (approximately) to expect payments, when I have meetings and phone calls. In addition, the calendar acts as my catchall scribble area. I always keep numbers and passwords there that I use daily but (for some reason) can't memorize. Longer numbers. Account numbers. Weird logins.
I also have a to-do list area on the calendar. This way, when I sit down, I don't mess around trying to remember what my next most pressing TO-DO was, but can just look at the list and get started.
Cork board: My cork board displays important information and short lists that I check on a daily basis. I have some specific AP style rules up there, the five "rules" I use when pitching magazines, and a list of articles I want to write for About.com. In addition, About.com requires certain elements in each article- I've got those outlined here. I also keep my thumb drives pinned to my cork board for easy access when I'm running off to teach a class without my laptop.
Current Projects Folder: I have a folder for each of these three: current projects, future projects and past projects. I keep associated paperwork in these. If a project is large and/or has a lot of paperwork, I'll give it its own folder, but it will still be nested within the current projects folder. However, it's important to note for these folders that only needed paperwork stays in there. Things like 1099 forms or contracts or other things that I simply won't be using are not kept anywhere near my desk. If it's not needed at hand, I file it away.
Laptop: My laptop organization consists of one main folder on my desktop that accesses all of my freelance writing business documents. The nested folders within there consist of Archives (where I store old projects and clips), Resumes, and Administrative items (logos, invoices, letterhead, my website pieces, photos for social media, etc.) The remaining folders at this level are individual projects, which each get their own folder. Once a project is done, its entire folder is moved to Archives, but not before I comb through it for some usable clips. I put my best clips in their own file for easy access for applying for new freelance writing jobs.
Files: My physical files hold hard copies of some of the same items on my laptop. The main folders are Past Projects, Current Projects (although this one is generally sitting on my desk), and Future Projects. In addition, I have a tax folder, a contracts folder and a To Read folder.
I hope that my systems and processes have given you some ideas for your own organization. Having an organizational system that works for you helps to maximize your hours. Many freelancers work only a few hours per day, yet need full time income. Having organizational processes in place can help you your income goals as quickly as possible.