Remember, keep the system simple. The benefits of a simple system based on consistancy, are obvious. As mentioned above, it helps you to find data easily. Another benefit of a simple system is that it allows others to find data easily. And very importantly, it keeps you from duplicating your efforts.
Nothing is more frustrating than having to look up a piece of data twice.
Section off your papers. You need surname sections. You should have sections for interviews, notes, census data, marriage data, birth and death certificates, maps, correspondence. Keep papers that you reference often separated from those that are archival in nature. For instance, photographs are best kept in the archival section of your files.