Man, this sure was a doozy. My company's product exposes web services via a Cassini-like web server, the types are exposed to the runtime similar to the way remoting objects can be registered.
This was all fine and dandy, but on Windows Server 2003, asp.net libraries do not work if IIS is not installed. We were about to lose a large business opportunity because this particular government entity required that IIS NOT be installed due to security policies.
Turns out the ASP.Net component under add/remove programs, which requires the IIS component, uninstalls ASP.Net if not selected. This can be reversed by running aspnet_regiis.exe -ir efrom the WINDIR\Microsoft.net\framework\v1.1.4322 directory. This installs asp.net on the system, regardless of whether IIS is installed.
Although the framework is built to be able to run asp.net outside of IIS, apparantly the creators of Windows Server 2003's component section didn't really care. Plus, the aspnet_regiis executable is pretty confusing since it does much more than simply register script handlers in IIS. But, problem solved.