Much to my dismay, once you make the move to the 2.0 .Net Framework, NDoc is no longer a viable tool to use for compiling C# code documentation into MSDN-style documents. Microsoft is picking up the slack here with the Sandcastle project. All of the documentation at this point seems to be in blog posts as well as their wiki. Here is a post on how to use Sandcastle. Also, several Sandcastle users have created scripts and tools that automate the documentation build process.
The September CTP release of Sandcastle is available for download.