Color Code Each Set:
In a effort to save money I use to always use white paper for everything. Now I copy each set on a different color if possible. There are some repeat colors but it's better than all white. There are two reasons for this. First, the students seem more excited when it's on color paper, like it's something novel and game-like. Second, when you find a stray card at the end of class it will be easier to determine which set it belongs to.
Write a Number of the Back of the Set:
Again, if you find a stray card on the floor at the end of class, you can use the color to find its home, but if there are more than one set with the color it can still be time consuming. Now I also number each set. So, one set will all have the number 1 on the back of each card, another set will have the number 2 on the back of each card, etc.
Laminate the Cards:
I don't know about your students, but I will always have one student who insists on writing on the cards, and then that set is ruined. Our department spent about $30 on a laminator and of course the cost of the laminating sheets. But I think it's well worth our sanity to not have to keep creating new sets each year.
Leave a Few Cards Blank:
For some of the cards, have some information missing. This forces students to think about the card sort. It also makes the card sort more than just a matching activity.
Store the Cards in Ziplock Bags:
I started by storing the cards in envelopes but I found two problems with this: the cards would fall out or some student would lick the envelope shut because that's what you do with envelopes. Now I use Ziplock bags, one bag for each set. Then I store the entire card sort in either a small labeled box or a large interoffice envelope (save those shoe boxes).
Another option is to store the whole card sort in a larger ziplock bag, tape the one end, and hole-punch the tape. Here's blog post with more details on that.
Store the Cards on Ring Clips:
After color-coding, numbering, and laminating, you might want to hole-punch the corner of each card and then keep them together with a ring clip instead of ziplock bags. Just make sure you don't hole-punch any important information.
Since publishing this post I've had a few more ideas with card sorts:
1) If you're using ziplock bags, I recommend piercing each bag with a safety pin. This way it's easy to get the air out.
2) If a card can be written in more than one format, do it. For example, I was looking at my card sort with domain and range.
Students match a graph with the domain of:
4 ≤ x < infinity
x ≤ 4
and [4, infinity)