I use a zippered binder by Five Star. In it I have two kinds of sheets: baseball card sheets (the kind you put baseball or trading cards in) and then I have sheet protectors (like you would use for a presentation).
I got a bunch of those binder separators at a back-to-school sale (you know, the kind with the little tabs on them) and use that to mark my categories. My categories changed over time as I learned the best way to separate coupons. Sometimes I would find myself hunting all over for a coupon, which indicated I needed a better category! My categories are things like: cosmetics, air freshener, yogurt, cereal, meat, dental care, etc).
I cut out little squares to put into the baseball card holders so I can put two coupons in each slot (one facing the front and one facing the back). Then I took the sheet protectors, put half of a filing folder in it and designated one store per sheet protector. Coupons and list for the week go in the front and store rewards (RR, ECB, etc) go in the back.
This took a little bit of time up front to set up, but it makes preparing for a shopping trip and taking advantage of unannounced clearance sales much easier. Also, it makes sorting coupons on Sundays a breeze. Sunday evening I'll pop in a DVD or pull something up on Netflix, and within an hour the coupons from my two papers are sorted (sometimes less if it was a sparse week for coupons).
Honestly couponing methods are highly individual. What works for me might not work for you. I tried using a little recipe box, but too many times of dropping the box had me searching for another method. Tried the clipless method with sheet protectors, but that left me frazzled. Finally the binder method really seemed to have clicked for me.
P.S. Sorry, I just realized how long winded this is. Hope you could follow everything!