I have put to the test Leonid's second suggestion, [ApplicationMaker][1] by [jmlopez][2], 
I have shared out an extended example [here][3]. It's a little library for rotation quaternions and rigid-body dynamics that illustrates the [Dzhanybekhov effect][4]. I created it from scratch by straight reading of the documents provided with ApplicationMaker (most of it in a very nice local cigar lounge, but that's another story :)  Here are my major findings:

You do `NewPackage` and get a notebook for writing your package (ApplicationMaker will make the .m file for you from this notebook). **Don't get even slightly fancy with usage messages in here!** In my first attempt, I tried something as little as setting the arguments for function forms in italics, and it caused a cascade of crap to happen later when I did `BuildApplication` and `DeployApplication.` I had to rekeyboard all my `::usage` messages because even one stray invisible `Italic` tag caused massive downstream pain -- missing styles, all kinds of `StyleBox` noise copied to the reference pages, many more goobers I didn't even look into.

Other than that, it seemed to work well with MMA 9, even though it was written for MMA 8. Huge kudos to jmlopez for working this out. While it's not perfect, it's such a great start that I will certainly use it in the future.  

I did not complete the documentation for my sample in the interests of getting this answer out quickly. Another couple of findings (really reminders for me) are:

Proper documentation is a **LOT** of work. It easily outstrips the effort of writing the code by factors of 2 to 10.  Even for my tiny example, it would probably take me several more days to get it to professionally presentable level.

**HOWEVER** it is very valuable work! The effort of writing documentation and thinking about how someone else would try to understand this tiny library made me improve it by refactoring and redesigning several times. A professionally presentable API isn't even fully DESIGNED before it's DOCUMENTED with a skeptical, third-party audience in mind! Just do it.

  [1]: http://stackoverflow.com/questions/6574710/integrating-notebooks-to-mathematicas-documentation-center
  [2]: http://stackoverflow.com/users/788553/jmlopez
  [3]: https://www.dropbox.com/sh/89z1vy6mgpxtayv/AADmZXYKEYlGNQqI_Fb8G2Zja/Dzhanybekhov
  [4]: http://www.youtube.com/watch?v=L2o9eBl_Gzw