I'll be honest. Organization is not my strong suit. So after a few months of researching my family tree, I found myself dealing with a growing mountain of papers-copies of various documents, book pages, articles and message board threads; notes; family group sheets; and printouts of items from the Family History Library catalog. It was time to break down and organize my paper mountain before it buried me. I'm still experimenting to find my perfect system.
Right now my system consists of my genealogy software, Family Tree Builder, file folders and an index card file. I use Family Tree Builder to organize all my date. Since it allows you to associate documents or pictures with individuals in your family tree, I'm in the process of scanning in these items. If I want to know everything I have, I run a report.
I broke down my file system into files for census, vital records, other documents (naturalization papers, obituaries, etc), family group sheets, articles and book pages, message board and mailing list threads, notes (which includes unproven rumors and speculations), and research items to check (a to-do list of sorts). As my family tree continues to grow, I will most likely be breaking these files down into subcategories, but for now, this works for me.
Finally, I have my index file. I bought the larger index cards for this. I basically use it to keep track of what sources I have for the individual. Since many of the names in my family tend to repeat through generations, I did decide to include vital statistics on the cards such as date of birth and death.
What is your system for organizing your research?