I would suggest taking a look at using Sphinx as a document authoring system - the results can be published as any/all of:
- HTML (including Windows HTML Help),
- LaTeX (for printable PDF versions),
- manual pages &
- plain text
Extensive cross-references: semantic markup and automatic links for functions, classes, citations, glossary terms and similar pieces of information.
Hierarchical structure: easy definition of a document tree, with automatic links to siblings, parents and children.
Code handling: automatic highlighting using the Pygments highlighter.
The inputs to the help system can be easily version controlled which is a big advantage.
Free, Gratis & Open Source but licenced for commercial use.