You can always enter JavaScript in text fields that allow HTML.
You will find a remark for those fields directly in ConfTool, such as "HTML elements may be used" (see image 1).
To add JavaScript to a custom phrase, you need to enable the Expert Settings.
Go to the bottom of the page for that phrase and switch the toggle from "Expert Settings Disabled" to active:
Overview -> Settings -> Wording and Phrases -> Edit Phrase (see image 2)
Only with expert settings enabled, JavaScript is allowed. Otherwise it will be filtered out of the updated text.
Please test your changes thoroughly!
Hint: Below you find a JavaSript example to open the link target in a popup window:
<a href="http ://www.your-conferencename. org/terms/"
target="page" onclick="window.open(this.href, 'Details', 'width=600, height=300, scrollbars=1'); return false;" onfocus="blurLink(this);">Link Terms and Conditions</a>