Hello clhs and welcome to the Seven Forums.
The only way to keep the software, applications and all the original bundled stuff from your Vista setup is to do an in-place upgrade installation. This way the Seven installation does not remove anything, it only replaces the system files and adds information to the registry.
However, if you choose (like you did) the clean install over a former Vista setup, all earlier system files, folders, installed applications and software are moved to this windows.old folder. This folder has two main purposes: it stores all users personal files and folders allowing them after installation to be moved to the respective user folders in Seven setup.
The second purpose is to allow restoring back to old Vista setup. About this you can read more here
Only portable applications and software in the windows.old folder can be used in Seven after installation. Basically, you have to reinstall all the programs you earlier had in Vista. Windows.old is not meant to preserve your programs to be used after a clean installation of Seven. It's only done so that restoring your old Vista setup would be possible as described in that article mentioned above.
Complicated. Here's the short version: You have to reinstall all the programs after clean installation. Most of your applications won't work even if you try to move them from windows.old to the Program Files-folder.