My paperscraps are kept in a binder like this. I've taken gallon ziplock bags, reinforced the bottoms and punched holes in the bottom.
I then have all my colors separated into bags. I do this only for my solid color paper. I find it works very well and that I use less paper then normal. When I need a little piece for matting I just go to my binder and find the color I need!!!!
As for my stamps, I have each and every stamp I own stamped out. I have them separated into categories; e.g. butterflies, sentiments, snowmen, etc......... I have a ton of clear dollar stamp sets from M's and I stamp them in a different color so I know which they are and where to find them. I find that it was well worth the effort to do this. I was not using stamps because I couldn't remember what I had. Now when I go to make a project I just look through my stamping catalog and pick my stamp out that way. It's also nice because you can actually see what it looks like stamped!
I hope my storage ways can help you out or give you some ideas about the different way's of storing things. Good luck with organizing! It can be a pain to start but you will be glad yo did it once your done!