Programs aren't just files dumped in a directory. They have shortcuts, registry entries, file type associations, and many other components depending on the program itself. They may also use shared folders (for example MS Office programs and many others) which they have dll files, or special resources they need to run.
You can't just turn your C into a storage drive, install a new OS on your new C drive, and pick up where you left off. You need to reinstall those programs.
This re-establishes all the other stuff along with it.
Do this: Rename you current "program files" directory to something else, say "progfiles"... Reinstall the programs as needed. Go into "progfiles" and copy over any relevant files, plugins, whatever, to the now-newly-repopulated "program files" directory. Once you have reinstalled and restored all your saved files, delete "progfiles" and all its contents.
You are now ready to continue as normal.
EDIT: Don't copy and paste entire program installation directories. Look for specific files you'll need and copy them over.
