For me, this was caused by my custom .desktop file. I downloaded
Firefox, unpacked it to my home and created a .desktop file for it in
~/.local/share/applicaitons as so:

    #!/usr/bin/env xdg-open
    [Desktop Entry]
    Version=1.0
    Type=Application
    Terminal=false
    Icon[en_US]=firefox
    Name[en_US]=Firefox latest
    Exec=/home/local/ANT/naddeo/firefox/firefox
    Comment[en_US]=Firefox directly from tgz
    Name=Firefox latest
    Comment=Firefox directly from tgz
    Icon=firefox

The issue was caused by my Exec line. I had to update it to this:

    Exec=/home/local/ANT/naddeo/firefox/firefox %u

Then external link clicks starting working again. I found that out by
looking at the .desktop file that the Firefox in the ubuntu repos uses
at /usr/share/applications/firefox.desktop and copying that.

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to libgnome in Ubuntu.
https://bugs.launchpad.net/bugs/1035221

Title:
  xdg-open/gnome-open opens blank firefox

Status in libgnome package in Ubuntu:
  Confirmed
Status in xdg-utils package in Ubuntu:
  Confirmed

Bug description:
  Both
  xdg-open http://google.com
  and
  gnome-open http://google.com
  result in a new Firefox window, with a single "empty" tab.

  This is not the expected result - I expect the page to open in a new 
tab/window. Running
  firefox http://google.com
  gives the expected result.

  Whilst I am seeing the bug under quantal (regression from precise) the
  packages xdg-utils and libgnome2-0 are the same version in both cases.

  "/desktop/gnome/url-handlers/http/command" is set in both cases to "firefox 
%s"
  --- 
  ApportVersion: 2.4-0ubuntu6
  Architecture: amd64
  Dependencies:
   
  DistroRelease: Ubuntu 12.10
  InstallationMedia: Ubuntu 10.04 "Lucid Lynx" - Alpha amd64 (20100217)
  NonfreeKernelModules: nvidia
  Package: xdg-utils 1.1.0~rc1-2ubuntu6
  PackageArchitecture: all
  ProcEnviron:
   TERM=xterm
   PATH=(custom, no user)
   LANG=en_GB.UTF-8
   SHELL=/bin/bash
  ProcVersionSignature: Ubuntu 3.5.0-9.9-generic 3.5.0
  Tags:  quantal running-unity
  Uname: Linux 3.5.0-9-generic x86_64
  UpgradeStatus: Upgraded to quantal on 2012-04-14 (117 days ago)
  UserGroups: adm admin cdrom dialout lpadmin plugdev sambashare

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