For your applications, you can go for a professional help system or roll your own. One example of the latter and made available for free or open source (license is unspecified) is Quhelp by developer Kostas Michalopoulos. Written in C, it parses html content files and merges them with a template.
There's an example of typical output using a tree directory which looks pretty good and that's also included with the source code. It's Linux compiled I think so you'll need Cygwin/Ming to build and run it on Windows unless someone cares to port it?
- Link to C Code Library
Hello, thanks for the reference
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The license is WTFPL and included with the source. I know its not a popular license, probably due to the name
but i thought it would be fun to use it. Besides, its probably the most liberal license ever written 
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As for a Windows port, i just released 0.2 with improvements based on comments from reddit and it includes a Win32 version (the original 0.1 also compiled with MSYS and MinGW though).