I want to install a site glossary using tooltip popups.
No problem finding tooltip popup scripts.

But obviously I don't want to code the same word every time it comes up on different pages to make it use the js.

Ideally I want to have a txt file with word+definition pairs.
(Would be no more than 2-300 words.)

Then when a page loads? something identifies any of those words. Visitors then view the word highlighted and can mouseover its tooltip popup.

Any idea what I can do?

I've written a jQuery plugin that will highlight words on a page that are found on wikipedia. It could be a starting point for you. The check if a word is on wikipedia can be changed to check a word in a textfile. Adding a link to a word can then be changed to your tooltip code.

http://www.pritaeas.net/public/jquery/hp/wikify/index.html

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