<p>Is there any way to generate project docs during automated builds? </p>

<p>I'd like to have a single set of source files (HTML?) with the user manual, and from them generate:</p>

<ul>
<li>PDF document</li>
<li>CHM help </li>
<li>HTML version of the help</li>
</ul>

<p>The content would be basically the same in all three formats.</p>

<p>Currently I'm using msbuild and CCNET, but I could change that if needed.</p>

Yes!
Use
SandCastle
to build CHM/HTM documentation of the APIs.
Use
DocBook
+
FOP
and other tools to produce other kinds of documentation in PDF, RTF, HTML etc...
They can be easily integrated with CruiseControl.NET through
NAnt
.