How do I transfer iPhone apps already on my computer to iTunes?

I'm a very tech-savvy person, but Apple products are something that I don't understand. I made the silly mistake of attempting to transfer my iTunes files from my PC to an external hard drive. That failed to work properly, so I attempted to transfer all of my files back over to the C: drive. My music and video files transferred back fine, but my apps will not show up in iTunes, even after pasting them into the "Automatically add to iTunes folder". How can I get my apps to reappear without repurchasing them?