Leo at LogSense has a hack on improving his Hipster PDA (using 3×5 GTD index card templates). He got himself couple of 1″ loose-leaf rings and a standard 2-hole punch with an adjustable guide. By using the loose-leaf ring, you can easily flip back and forth and add new cards easily:
This made my life much easier. Now I can continue to carry my cards with me in an organized fashion, and I can use both sides and flip them back and forth. The important part is to use the punch guide always at the same level, so the holes are always aligned.