Program Files (x86) is for 32-bit applications. The x86 is somewhat outdated now, but it refers to the family of Intel processors, starting with the 8086, followed by 80186, 80286 and 80386 - and the 486 and then the Pentium. The main Program Files folder - without the x86 - is for 64-bit applications, of which there are still only a few. Most applications have not yet made the transition and are available as 32-bit only.
Some programs (Internet Explorer is one) come in two versions. The 32-bit version, which runs by default, is in PF86 (pardon my shorthand); the 64-bit version is in PF. To run the 64-bit edition, you can browse to C:\Program Files\Internet Explorer\iexplore.exe and click on it; you can also create a shortcut or pin it to your Start menu, just like any other application. You can even run both versions of IE at the same time, each running from its own PF folder.
It is best to keep BOTH versions and not try to save disk space by combining them because each uses its own version of certain .dll files, drivers and other support files, stored in the separate Program Files folders.
When I first saw the (x86) folder in Windows XP x64 several years ago, I guessed wrong about it and tried to put my 64-bit programs there for about 6 months before I learned its true meaning. Things got very tangled because I was still dual-booting with 32-bit WinXP Pro and tried to run a single set of executable files for Microsoft Office and other programs from the PF (no x86) folder. :>( Please don't make that mistake!
In time, as 32-bit apps fade into history, the (x86) folder will disappear,
I suppose, but I expect it will take several years.
References :-
http://www.vistax64.com/vista-file-management/218219-2-program-folders-64bit-vista.html
http://www.tomshardware.com/forum/3885-63-folders-program-files-program-files
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