Implementing cross-platform help system

Although I use a Mac almost exclusively, I write cross platform apps for scientific calculations and visualization. Up until now, I have simply distributed a PDF of a users manual to help users get started, but I would like to give my users more immediate, and hopefully built in access to help. So, I have prepared as set of html files with help information. The questions is, how to integrate those files with the application.

I know that I can use a program like App Wrapper Mini to embed the help files in the application package on the Mac, but what is the convention on the Windows side? I could just add a simple html viewer to my application to display the help files but is there a more standardized way of delivering help in Windows and what does one need to do in terms of post-processing the app to deliver that functionality (hopefully using the same html files that the Mac side uses)?

Excellent question! Looking forward to responses from developers more knowledgeable on this topic than I.

For the IDE we have all the HTML , images etc in a database and just load the appropriate HTML when you select an item in the IDE or navigate using the local reference

Most people expect the help system to be native to their platform. Obviously there are exceptions to this rule, but a lot of people expect it. There are a couple of tools out there that will help you compile for each platform:

Look on the Third Party Products page for some Help Authoring tools that will work on Mac and Windows help systems and beyond.

Thanks, all, for the suggestions. There are indeed some very useful 3rd party extensions. As an academic who writes free software for other academics, most are beyond my needs/budget, but I can see how they would be useful in other contexts.