Funny, I was recently adding help to an old NetBeans-based image/vector editor I've been toying with updating, and the idea of using Javadoc simply made me ill, so I wrote the beginnings of a help system from scratch, where help is generated in code annotations in Markdown, which an Antlr parser and some Swing magic render directly to the screen without ever translating to HTML. It's a work in progress, as I have another project I'm trying to wrap up.
Many years ago, when Sun open sourced it, I had the joy of converting the code to Ant and making it open-source-friendly. It was old, long-in-the-tooth and rather vile then - at best, it's an ugly (the classic Swing "border buildup" issues) clone of 1990's era Windows Help. It is long past time for it to die. It's one of those things nobody actually likes, but nobody actually wants to write a replacement for either. I imagine it wouldn't be that hard to write something that can consume the existing input files, but something simple, modern and that either uses the user's web browser, or at any rate doesn't demand in-application HTML rendering, and doesn't require HTML as its markup, would be a good idea. -Tim