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A pop-up window displays whatever title tag is in the HTML document that it loads. So that spot (the title bar of the pop-up window) is handled in the html doc that loads.
Or are you hoping to control the title attribute that shows on mouseover, before the pop-up launches? If that's the goal, you can write:
<a href="poppage.html" onClick="popupFunction();return false" title="Whatever You Want">Link Text</a>