I have Windows 7 Professional 64-bit on my MacBook Pro. The two Program Folders are dedicated to either 32-bit apps or 64-bit apps. Many apps are built for 32-bit so a lot of them are going to install in the x86 programs directory.
The only apps that I have in the dedicated 64-bit programs directory are ones that I have picked specifically to have as a 64-bit, such as:
- Bonjour (I believe from picking the 64-bit iTunes installer)
- Boot Camp drivers
- Paint.Net
- Certain components of Office 2010
Because I have 64-bit Windows, I can't install older 16-bit games so I either use DOSBox for DOS-based games or a Windows 98 virtual machine for Win9x games.