Spare buttons come with many new clothes and the age old question of what to do with them often pops up. I did some research and found an article from Real Simple magazine (June 2012) that suggested labeling the small plastic bags they come in with a sharpie and storing them in a button box or sewing kit. This is good, and for most people, good enough.
If you are really looking to hit this one out of the park, you may want to consider grabbing a binder, some plastic business card sleeves, and printing out some label inserts as shown in a blog post on a website called modernparentsmessykids.com. Click here for more details on how to. (Scroll about 2/3rds of the way down the page.)
Either way you do it, you will thank yourself when a button goes missing on your favorite cardigan sweater.