The new HTML help system has lost the functionality of annotating help topics (it is on the list of items to be added hopefully to the next version), but the favorites page adds a whole new ability to create more useful help.

Drag a URL onto the favorites page, like www.levelextreme.com and the UT available right inside of Help!

Create your own file of tips, help, annotations either as a .htm file or .txt and drag it into the right pane of the viewer.

Drag a .doc or .xls or .htm or visio drawing file in there, a simple click of the add button and the file is right there at your fingertips.