One of the best things I have found for organizing wooden stamps is a project case, which is available at most office supply stores and is sometimes available at organization stores and craft stores.
http://www.amazon.com/Clear-Document-File-Project-Case/dp/B00008XPQF/ref=sr_1_1?ie=UTF8&s=home-garden&qid=1266352042&sr=8-1
You can use one case for each category you want to designate -- the stamps lie flat in the case so you can see all of them. And then I put labels on the cases so it is easy to find what I am looking for.
I find I am using more clear stamps lately, which is great because they take up less space than wooden rubber stamps.
For clear stamps, I have found this product that works well, the See-Ez Purse Book.
http://www.joann.com/joann/catalog/productdetail.jsp?pageName=search&flag=true&PRODID=xprd623671
I know some people prefer to store clear stamps in binders or in CD jewel cases, so you can see what works best for you.
I have weeded out stamps that I am no longer using and have sold them at a local stamp store's used stamp sale. You could also try selling them at a garage sale or donating them somewhere. I think it is worth the effort to remove the stamps you don't use so you can easily see and manage the ones you do still want to use.
