Here are a few different ways:
The Envelope Method (I have used this for a long time) this is a cheap (ie. free way to organize your coupons) just reuse envelopes that you got your mail in. Organize by catagory,store whatever.
The Coupon Organizer (I recommend one for each store and/or one for food products and one for non food products since not all will fit in just one - I have done it both ways)
The Box/Container Method (cut out all coupons and organize and keep in containers then go through prior to going to the store)a good way to use up those baby wipe containers - make dividers for the inside and/or use paperclips to clip like items together
Currently I am doing the last two. Was just recently doing the first and last but since I bought those nifty coupon holders at Target I went ahead and upgraded. :)