Small ziplock bags are doing the job for me right now. I was standing in the check out line at Hobby Lobby when I spied them. 100 little bags for $1.99! When I am feeling the need to be super organized, I use a large safety pin and pin bags with similar colored buttons together. I have one small drawer for "most likely to be used" buttons and separate drawer for "if I ever need an odd button."
Do you have a neat way for storing buttons that you would like to share?