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[meyerweb.com...]
Elsewhere... there are "Information balloon pop-ups"
Also note that the IE "active content warning bar" is more intrusive when you are running files locally without a local server. Javascript pop-ups served online from a click rather than a hover are not so problematic.
You're saying that as individual html pages, my 100 (approx) glossary definitions would all be out there 'working for me'
Yes, if you code them with search engine bots in mind, these small pages can be an asset. Give some thought to any search traffic that would come directly to that html page, but not displayed in a pop-up window. They'll need some navigation to get into the main pages.
The anchor tag that calls the pop-up script should also include a regular html link -- for user agents that do not run javascript. Then the actual javascript pop-up function call should end with ;return:false; so that the main page does not also load the definition for those who have javascript turned on.