1. For some programs it might work to just make new shortcuts to them and (if needed) redefine their file associations.
2. For other programs you'll need to re-install them. Use the latest download if possible. Otherwise use the cd or dvd you bought or burned, or the original download that you saved on your backup (you did, I hope) together with the original license code if not freeware (you saved that, I hope).
I upgraded to Windows 8 last night, and encountered a lot of problems. My dual screen was not working, all drivers had been lost. However after upgrading to Windows 8.1, thankfully some have been fixed. However my biggest problem is that I have lost all my programs even though I installed it on a different partition of my hard drive.
So when I was upgrading to Windows 8 from Windows 7, I did a custom install. I formatted my C:Drive since there wasn't enough memory. I thought I would have kept all my programs since it was installed on another partition, but after the setup was complete all my programs were gone, though they still showed up on the D:Drive. Luckily I copied all of my C:Drive to an external drive (Copy and Paste) and so I thought of just copying it back to the new C:Drive, but that didn't work.
How do I get all my programs back? It's still on my D:Drive, but it isn't showing at all so in order for me to launch it, I have to manually go to Program Files (x86) or Program Files and fine the desired program which is a bit of a hassle.