To allow google to crawl those pages linked to with javascript window.open commands, and allow for users without javascript to browse those pages---use something like this for your anchor tags:
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<a href="index.html" onclick="window.open(this.href,'popper','scrollbars=1,width=325,height=500'); return false;" onkeypress="window.open(this.href,'popper','scrollbars=1,width=325,height=500'); return false;">
This will allow you to utilize all of your javascript popup window control, while still allowing web crawlers and noscript users to navigate the content in your popup windows.

