I'm taking two genealogy classes right now at NIGS. One is Methodology Part 2: Organization and Skillbuilding. Among many other things, I've learned many ways to make my genealogical life much, much easier. Here are some of my favorite suggestions for organizing your research:
Color-coded binders Keep your important paperwork in binders, in page protectors, and have different colored binders for each family line. I actually just use color-coded labels - it's cheaper than trying to find the right color binders.
Research log Keep one for each person that you research, recording both successful and unsuccessful searches. This prevents you from wasting time in a place that you've already searched. Since I started researching before I knew what I was looking for, I haven't kept tabs on this information as well as I could have.
Organize your correspondence I never realized how many information requests I would send and receive. Keeping a correspondence log of your information requests ensures that you don't ask for the same information twice. You'll also know what requests have not been answered - both incoming and outgoing - so that you can do the necessary follow-up.
Other forms Find or make the forms that will be most useful to you, and be consistent when you fill them out (always use the same name and date formats, abbreviations, etc.). Software programs can keep track of a lot of information for you, but recording your research problems on paper can help you organize your thoughts and have all the information you need handy, no matter where you are researching. I especially like the idea of having a form to sketch out difficult research problems, including all the information you already have, and specifying what you are trying to find out.
Cyndi's List has compiled a great list of free forms and charts designed to help you organize your research here.
I'm really enjoying my classes so far. The second class that I'm taking is Electronic Resources: Using the Internet. I'll be reflecting on them both a great deal in the near future.