The number 86, is in reference to the part numbers for Intel processors.
(4004, 8008, 8080, 8086, 80286, 80386... after a while the 86 part begins
to stand out.) It has become synonymous with the instruction set used on
Windows PCs. And in this particular case, as Andy points out, it means
"32 bit stuff".
AMD did instruction set extensions for 64 bit sized instructions,
and x64/AMD64/EM64T all refer to those kinds of extensions.
Your typical modern processor now, supports both kinds of instructions
at the same time. That is how it is relatively easy to run 32 bit
programs, from within a 64 bit OS, as well as running 64 bit programs.
There aren't a lot of 64 bit programs, and an example of one, is the
availability of both 32 bit and 64 bit versions of Internet Explorer,
on the same machine.
When both 32 bit and 64 bit programs are staged on the same machine,
it's handy to keep them in separate folders. Presumably for the
benefit of humans, as the machine knows what they are. (32 bit ones
are PE format, while 64 bit ones are PE+ format, which stands for
portable executable. As far as I know, the loader can tell what they are.)
http://en.wikipedia.org/wiki/PE_executable
There are some programs now, which are only available in 64 bit form.
Adobe sells some like that. Presumably, to piss off the people
running a 32 bit OS.
Paul