Resolved Empty Programs left in Start/All Programs, Not in Programs File

PC's registry was so messed up recently that even my programs .exe files were compromised.
I decided to completely uninstall the problem programs: AutoCad, MS Office XP pro, MS Pub 2003, and Quicken.
I have used perfect uninstaller, Eusing Free Registry Cleaner and CC cleaner.
Concerned that there are still many empty programs in Start, and the Start Folder doesn't include even all the installed programs.
How can I check and edit this in the registry safely?

 

Why wouldn't my C: Programs or Documents and Settings communicate or connect with the programs in the start menu? They should, and I want to fix this.

 

Just not sure which files are responsible for posting and editing the program shortcuts on the start menu. It saves a lot of time when you are trying different downloads all the time.