You can just put a "span" around the link and set the "title" attribute to whatever you want the hover text to be, like this:
<span title="Hover text">[[test]]</span>
That should do the trick for most things.
You can also use HTML Attributes to do the same with a HTML anchor element, however this will cause the related Passage Connection Arrow to disappear on the Passage Map if you are using one of the Twine (1.x or 2.x) applications.
<a data-passage="test" title="Hover text">Test</a>