Haha, we had a long winded discussion about this on our site, I think this is pretty close to their thinking.
Pop-ups are getting deprecated and when someone chooses to implement it in their site they are simply shooting themselves in their own foot for not being Browser and Device Independent; really, W3 discourages it and provides alternatives. Thus, don't expect these on a mobile browser.
It's the developer that has to adjust; not you, the user that has to figure ways around standards. At best you could figure out the URL that is being opened in the pop-up on a computer, and open that URL on your mobile phone. But other than that, the site you're browsing is outdated and isn't made to support the mobile world...
typical M$ rubbish, our way or the highway!
Still, back to the original question, can anything be done on our end?
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Joined: Jun 29, 2004