When should I put programs in "Program Files" and when "Program Files (x86)"?

Looks like you are using a 64-bit version of Vista (as am I). It should do this automatically but here it is:

64-bit in program files, 32-bit in the x86.

The separation is needed at times and should be withheld: http://www.winvistatips.com/2-program-folders-64bit-vista-t171602.html

I don't believe it really matters because some programs that are 32 bit, will install in the Program Files (even though that's what the x86 folder is for). I believe its just for organization. So best practice would be

• 64 bit= program files
• 32 bit= program files x86