I think he means that after reinstalling Win XP Pro it kept he's old program files, which are still in C:\Program files. The problem is that none of them are in the add\remove programs in the control panel or on the start menu. So how does he get them back to the add\remove programs and the start menu.
I think you'd have to reinstall\repair them as the registry keys for them are missing. The links for a user on the start menu would be in C:\Documents and Settings\"UserName"\Start Menu\Programs as .Ink files. For all users there in C:\Documents and Settings\All Users\Start Menu, in the same format.