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I agree with Rockintom. I also use legit pop up for some designs (IE onClick pop up windows). I use a turnaround JS code I found here for both browsers and search engines. I use this on the link :
<a href="file.htm" onClick="window.open('file.htm','','scrollbars=no,resizable=yes,menubar=no,toolbar=no');return false;" target="_blank">Link to file</a>
And this on the body tag of the targeted page :
It does not do anything for menubar, toolbar and window position, but at least all visitors get something with a pop up killer or with JS disabled. I try to give a good margin to window size around elements, so visitors with pop up killers get to see it all without resizing the window.
Check [lavasoftusa.com...] for Ad-Aware (free), which does a good job of identifying and removing scumware components.