The Eclipse help system changed dramatically in Eclipse 3.3, and it requires a new set of plug-ins to work correctly. There is little documentation about how to include the help system in an RCP application, though Kai Tödter was kind of enough to post a list of the correct help system plug-ins.
I’ve taken that list and pared it down a bit (the Ant plug-ins are not necessary), and created a simple working example of an RCP app with integrated help. The example wraps the Eclipse help system in a feature called org.eclipse.help, which you can reuse in your own applications. There is some talk about making the help system an official feature in Eclipse 3.4, but for now the included feature should get you what you need. You’ll of course need to add the required plug-ins to your target platform, and if you’re curious, this is the final list:
To get started, just download the example projects and import them into your workspace.