There are a few ways to organize coupons that I know of. There is the "Filing Method," "Clipless Method" and "Binder Method." With each method, you may also include a coupon-insert list of the coupons for each week. This is my favorite place to get one. (The coupon website I look at has a printable list. I live in the northwest, and my favorite couponing site is Fabulessly Frugal.)
The Filing Method utilizes manilla folders. Each week, you create a new folder for each coupon insert (Smart Source (SS), Red Plum (RP), and Proctor & Gamble (P&G)) that includes the date and name of the insert.
The Binder Method is where you clip out all the coupons each week and put them in baseball card protector sheets. The coupons are categorized so it is easier to find the coupon you are looking for. If you are interested in making your own, I have a little tutorial here.
The Clipless Method is a mix between the Filing Method and Binder Method. Each week you would take the inserts and put them in 8.5" x 11" sheet protector and write the date on the front. The sheet protectors are organized in a binder.
There are pros and cons to each method. I have tried the Clipless Method as well as the Binder Method. I prefer the Binder Method. It does take time to clip coupons each week, but I think it makes couponing go much smoother. (Different people prefer different methods. You may have to try different ways to see what works for you.)
Here is a link I found that goes more in-depth with each method.