One of my bridesmaids suggested numbering each person, couple, or family in our master spreadsheet and then writing that corresponding number on the reply card in their invitation. This way, if you lose a reply card or someone forgets to write their name on the card, you're in luck! Just reference the number on the reply card (or figure out which one is missing). Here's a picture of the invitation process and numbering.
That's a lot of paper!