I only have clear stamps since I just got into stamping.
What has helped me is......... A 4" binder at Office Maxx, acid free transparencies, and 8.5 x 11 page protectors.
I get however many stamp sets in a theme (i.e. halloween, birthday, fonts) I can on my transparencies then put them into the page protector. This way is something falls off its at the bottom of the protector.
When I want a particular set I just pull out the transparency and lift off that set or I can pull out the entire transparency and use all the sets on it. Its easy to find and easy to put away!
As my collection has grown and I needed further organization, I found that Avery now makes really sturdy repositioning tabs that can be written on. I used those like a divider on the edge of the page protector.