I had this clothing fix-it kit idea sent to me a couple of weeks ago in my daily Martha Stewart newsletter (sorry, I know I've been harping on Martha a lot lately), and I thought it was such a great idea! All you need is a pack of business card organizers (I found mine at Staples), a binder and your buttons.
As you can see in the picture, Martha kept her extra threads as well. However, my inability to sew or knit means I don't ever attempt to patch up any holes in my sweaters and thus have no need for the extra thread often supplied with them. I always toss that part out and just keep the buttons. You gotta have the buttons.
Clothing Fix-It Kit
I took my fix-it kit a step further by organizing the buttons by type and color so I could easily locate them, but if you're not as OCD as me, just sticking them in a sleeve is good too.
When you're done, you'll have a neatly organized kit and a designated place for all of your extra buttons. You can also fill the binder with any other tid bits you've been collecting that need a home.