Randy Seaver in his Blog Genea-Musings has written an interesting article on his project to organize his paper genealogy files. It is well-written and easy to follow.
Randy's approach follows some of the guidance offered by another genealogy Blog, DearMYRTLE. He even give links to several articles dealing with organizing found on that popular Blog. This is not the only way to get organized, of course, but it may give you some ideas of your are wondering what to do with your own collection.
You can read Randy's article at http://goo.gl/i7GAh