The Eclipse Rich Client Platform (RCP) is very powerfull, and takes a lot of architectural things of your hand when developing a bio- and chemoinformatics GUIs. Bioclipse is based on it. One thing the RCP offers is a Help View which works with plain (X)HTML files, and one neat feature is the context help. It is help shown in the Help View when one focused on a specific GUI element.
As an example, the below figure gives the context help for the JmolView in the Jmol plugin (bc_jmol) plugin for Bioclipse:
On the right side of the Jmol view (showing 1SPX) is the Help View, showing the context help for the Jmol View pointing to the 'Jmol Script Commands Reference'.