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I'm using the popups to ease navigation on my website, for documents and movie clip.
Thank you
<a href="yourpopup.html" onClick="popUpWin('yourpopup.html'); return false;">Details</a>
or
<a href="yourpopup.html" onClick="return popUpWin('yourpopup.html');">Details</a>
Where "popUpWin()" is your Javascript that creates the pop up window, and the passed parameter can be a document or an image. In the second example, the function must return false or the page will move to the link specified in the href.
The "return false" will only stop the click event from following the link specified in HREF **IF** Javascript is enabled. So a search engine, which is most likely not going to trigger this event, will follow the HREF and access your content.
Too often "popup" is confused with popup ads from window onloads. I don't think there's any penalty for user-initiated popups, as long as you allow access to the content if Javascript is not enabled.
But I could be wrong, as I'm about to find out. :-)
Edit: Oh and by the way, welcome to WebmasterWorld!