What is difference between Program Files and Program Files(x86) folders in Windows 7 ?

The difference between the two is that "Program Files" is used to install softwares which are 64-bit softwares and "Program Files (x86)" is used to install softwares which are 32-bit softwares.

This is the default behavior. So if u find any softwares under "Program Files", remember they are 64-bit softwares and vice-versa.