I have to retract my previous statement. Either I wasn't paying enough
attention or the behavior changed. When I went changing Preferred
Applications setting around, Firefox stopped taking focus unless "Open
link in new window" was set. However, I found that Compiz has a setting:

/apps/compiz/general/screen0/options/focus_prevention_level

that when set from default of 1 to 0 (off) Firefox now takes focus. Also
found this bug:

https://bugs.launchpad.net/ubuntu/+source/ubufox/+bug/272171

where someone mentions the same thing. Even if you're not using Compiz
you might want to check the window manager settings to see if there is
one that fixes it for you.

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