Now I've discovered that this same problem occurs with Chrome as my default 
browser. And it happens the same from other source applications such as 
terminal or nautilus. So it is not an issue with any of these apps in 
particular, which makes you think it's a GNOME problem. But then here's a post 
where someone claims to have the same issue in Kubuntu 10.04:
http://ubuntu-virginia.ubuntuforums.org/showthread.php?p=9265170

My entire workflow pretty much consists of getting notification emails
from some web app and clicking a link to go to said web app to continue
working. This new behavior is thus pretty maddening, and I would like to
help fix it however I can, but I don't know which direction to keep
investigating at this point... where does the focus-or-not decision even
get made??

-- 
focus does not switch to firefox when a hyperlink is clicked in another 
application
https://bugs.launchpad.net/bugs/546969
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