I had to use a recovery CD to reinstall windows. Now my desktop is generic. I have all of my programs in the directory etc.

How do I get these user settings back and the ability to use my programs again?

You will have to reinstall the programs.

That's the major headache if you used your system CD's to reinstall windows other than repairing or running a checkdisk..
Once you ran the installer, formatting the hard drive, your information is lost.