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[Sean Fitzpatrick <sean.fitzpatrick@xxxxxxxxxxx>]

I am also seeing the old legacy notification icon for Empathy, and can find nowhere in the settings to remove it.  Of course, you can get rid of the old icon by removing empathy from the systray whitelist using dconf-editor.  But for me it's easiest to set that to 'all' because I have a few programs that aren't whitelisted by default that use the old notification area.
There used to be an option in empathy that hid the speech bubble icon (so only the envelope is left) but I no longer see such an option.

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https://bugs.launchpad.net/bugs/864661

Title:
  Remove empathy notification icon redundancy in Ubuntu 11.10

Status in “empathy” package in Ubuntu:
  Confirmed

Bug description:
  After upgrading to 11.10. A redundant notification icon appears. There
  is no way to remove this and it's function is completely redundant
  since the inclusion of messaging menu in the indicator applet of
  11.10.

  ProblemType: Bug
  DistroRelease: Ubuntu 11.10
  Package: empathy 3.2.0-0ubuntu1
  ProcVersionSignature: Ubuntu 3.0.0-12.19-generic 3.0.4
  Uname: Linux 3.0.0-12-generic x86_64
  NonfreeKernelModules: nvidia
  ApportVersion: 1.23-0ubuntu2
  Architecture: amd64
  Date: Sun Oct  2 15:49:21 2011
  EcryptfsInUse: Yes
  InstallationMedia: Ubuntu 10.10 "Maverick Meerkat" - Release amd64 (20101007)
  ProcEnviron:
   PATH=(custom, user)
   LANG=en_GB.UTF-8
   SHELL=/bin/bash
  SourcePackage: empathy
  UpgradeStatus: Upgraded to oneiric on 2011-10-01 (0 days ago)

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