At OSNews.com the article Windows x64 Watch List describes some of the key differences between 64-bit and 32-bit Windows. It's pretty interesting, and mostly pretty reasonable. But this one caught my eye:
There are now separate system file sections for both 32-bit and 64-bit code
Windows x64's architecture keeps all 32-bit system files in a directory named "C:\WINDOWS\SysWOW64", and 64-bit system files are place in the the oddly-named "C:\WINDOWS\system32" directory. For most applications, this doesn't matter, as Windows will re-direct all 32-bit files to use "SysWOW64" automatically to avoid conflicts.
However, anyone (like us system admins) who depend on VBScripts to accomplish tasks, may have to directly reference "SysWOW64" files if needed, since re-direction doesn't apply as smoothly.
I've been using 64-bit Linux since 2005 and found there to be some learning curve there, with distributors taking different approaches to supporting 32-bit libraries and applications on a 64-bit operating system.
The Debian Etch approach is to treat the 64-bit architecture as "normal", for lack of a better word, with 64-bit libraries residing in /lib and /usr/lib as always. It's recommended to run a 32-bit chroot with important libraries in the ia32-libs package going into /emul/ia32-linux. Ubuntu is similar, but its ia32-libs puts its ia32-libs files into /usr/lib32.
The Red Hat approach called "multilib" keeps 32-bit libraries in /lib and /usr/lib with new 64-bit libraries living in /lib64 and /usr/lib64. (I mentioned this a while back while discussing building a custom Perl on 64-bit Red Hat OSes.)
Each way has its tradeoffs, and causes a bit of trouble. That's just the cost of dealing with multiple architectures in a single running OS, where no such support was previously needed.
But the Windows way? Putting your 32-bit libraries in C:\WINDOWS\SysWOW64 and your 64-bit libraries in C:\WINDOWS\system32? It hurts to see the names be exactly backwards. That's really tops for confusion.