Comment 5 for bug 546969

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.