What is a good tool for writing a user manual (help file), which integrates with version control

DocBook

_{(source: docbook.org)}

Microsoft HTML Help Workshop can be used to create good quality professional CHM help files. All you need is a bunch of HTML files. The tool "compiles" all these and bundles into a single Help file. The HTML files can be generated using Microsoft Word/Frontpage or even Dreamweaver. You might want to consider source controlling these HTML files.

Latex. Lyx provides WYSIWYM for writing latex files.