When most of Apple's stuff was deployed OS X client wasn't very mature, let alone the server. If stuff is deployed and stable and working, then it tends to get left that way.
For Apple's developer site, they send back this:
Server:Apache/2.2.9 (Unix) PHP/5.2.6 mod_ssl/2.2.9 OpenSSL/0.9.7l mod_jk/1.2.25 mod_perl/2.0.2 Perl/v5.8.8
So they use php on the backend for the developer site and WebObjects (Java) for their store and other areas.
For their homepage and other areas, they just send back this:
Server:Apache/2.2.9 (Unix)
The Apache could be running on any UNIX like system.
CUPS is hosted on Red Hat:
Server:Apache/2.2.3 (Red Hat)
All the other Apple sites (Webkit, Mac Ruby, Mac OS Forge) send this back:
Server:Apache/2.2.11 (Unix) mod_ssl/2.2.11 OpenSSL/0.9.8k DAV/2 mod_python/3.3.1 Python/2.5.4
I've read the use a combination on Sun Servers and XServes for MobileMe.
The whitehouse.gov sends back this:
So you know they're on Windows Server.