It's a hidden system folder for holding certain types of program data.
How does it differ? If you look through it, you will see that it
doesn't have all the same folders as Program Files, nor do the folders
have the same contents.
I've only been using Vista on my HTPC since last August, so my memory is a
bit hazy, but I think that folder is used for apps that write to the Program
Files folder, and so are not UAC compliant (or multi-user).