Ran into the same issue and researched this for a few minutes.
I was taught to use Windows 3.1 and DOS, remember those days? Shortly after I worked with Macintosh computers strictly for some time, then began to sway back to Windows after buying a x64-bit machine.
There are actual reasons behind these changes (some would say historical significance), that are necessary for programmers to continue their work.
Most of the changes are mentioned above:
Program Files
vs Program Files (x86)
In the beginning the 16/86bit files were written on, '86' Intel processors.
System32
really means System64
(on 64-bit Windows)
When developers first started working with Windows7, there were several compatibility issues where other applications where stored.
SysWOW64
really means SysWOW32
Essentially, in plain english, it means 'Windows on Windows within a 64-bit machine'. Each folder is indicating where the DLLs are located for applications it they wish to use them.
Here are two links with all the basic info you need:
Hope this clears things up!