Two options:
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).