I'm working with David Allen's "Getting Things Done" method (GTD) and my PDA design reflects that. I use the to-do list template for my "next actions"...
Step 5: PUNCH some holes
Using the hole punch, punch two holes in each card. If you are using a single hole punch, try to get the holes the same distance from each end, about 3/4". If you are using a double hole punch, try to get the holes centered on the card's edge. The reason is so you can later flip over the card and use the other side. If the holes aren't symmetrical, the card will stick out from the others.
Here's a tip: Start with just one card and then use that as a guide for punching the rest.