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If you are using CHM files, you can use the "merged CHM" construct to make a flock of help files look more-or-less like one. OK, it's HTML Help so it's flaky and a bit buggy, but we've been using this method with good results for quite a long time. You don't have to write code to support this: tools like Flare and RoboHelp have support built in.
It might help if you gave us some of your constraints or assumptions. Do you want to end up with hardcopy, PDF, Web help, CHM files? Are there any tools you need to use, are expected to use, or can't afford to use? Some of the possible solutions are technology-independent, but if you find that the best answer really is a tailored doc set with just what the user has ordered, the technologies to be used are important.
Other variables that might constrain the solution are: Can the users buy modules after the initial platform purchase? Can modules be versioned independently?
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Writer Tip: Create 10 different outputs with Doc-To-Help -- including Mobile and EPUB.
