Some of the enhancements you can make to an HTML Help file are useful, and some are not. The following are my recommendations of HTML Help changes in order of priority.
Information types enable users to select information that pertains to them. When you mark text or topics with information types, the information can be shown or hidden depending on whether the user selects to view that information type. For example, you can set up an "Administrator" information type for information that pertains to administrative users. If a user selects another information type, you can set the Administrator information to disappear.
Dynamic HTML (DHTML) enables you to show and hide information based on users action at that topic. For example, a user can click on text to reveal additional text. (See Step 1 for an example.) You might consider using DHTML in place of popup definitions so that the definition appears in the body of the text, instead of a separate popup.