WebAuth (cf developer link) can be built cleanly on Mac OS X Server 10.6 with no additional flags or configuration edits. Just ./configure, make and sudo make install. Because of the changes in Snow Leopard server, you can now use WebAuth while continuing to use Apple's Server Admin.app tool to manage your web server.
This is different than with Mac OS X 10.5, which has an httpd built with 64- and 32-bit PowerPC and x86 architectures. WebAuth, like many other Apache modules, did not build properly, since each module needed to be of four architectures, too. (Instructions for Leopard Server are here. For instructions on installing WebAuth on other Unix-like operating systems, see here.)
Here's a list of things that are, I think, unique to the process of installing and using WebAuth on Mac OS X Server 10.6, after the jump.