Sandcastle has a fairly complex XML MAML for generating Conceptual Help, as discussed in a nice intro from 2007. How does this compare to Doxygen in terms of ease of writing content and control over generation of the pages?
I am a big fan of using the Doxygen page facility to write such conceptual help including discussions of design issues. It is much less structured - there's the main page and you can then choose how you group pages by adding links with subpage or ref commands.
I also like the fact I can include casual Graphviz diagrams in my doxygen pages either with inline fragments or referring to an external file.