Supporting 16GB of memory doesn't mean 16GB will be available to 32-bit operating systems (XMP is a user-friendly overclocking aid). If your peripherals are 32-bit, they get mapped into the lower 4GB of memory. The leftover physical memory is then remapped above the 4GB boundary, inaccessible to 32-bit operating systems without some means of accessing it, like PAE.
Anyhow, you're running 64-bit operating systems, so it shouldn't matter. If you do decide to go 32-bit, use Windows Server 2003 Enterprise and add the /PAE switch to the appropraite boot.ini string.
I don't run 64-bit Windows for two reasons: 1) no DOS virtual machine (I know, I could use Virtual PC, VMware, etc., but I like NTVDM); 2) no 64-bit Catweasel drivers.
I use Cygwin and Microsoft Services for UNIX (the descendant of Interix, a replacement for the POSIX subsystem bundled with Windows) for most of my UNIX-like needs. Cooperative Linux (coLinux) is great, too, and I prefer Gentoo when I actually run Linux on x86.