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The notification area, when I customize it, still shows three programs and their icons. But they can not be seen if I customize to show them. They are not possible to remove from the list.
The programs are uninstalled, the registry cleaned, no leftovers there. So... how to remove these icons from the list for the tray after the programs are removed? Once again, the registry is also clean! Where are those icons/info hiding?

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This article explains how to do it:

How to Clear Customize Notifications (System Tray) Icons in Windows 7/Vista and XP

To clear the Customize Notifications items list manually, follow the steps below:

  1. Click Start, type regedit.exe and press {Enter}
  2. Navigate to the following branch:

    [Windows XP]

    HKEY_CURRENT_USER \ Software \ Microsoft \ Windows \ CurrentVersion \ Explorer \ TrayNotify

    [Windows 7 & Windows Vista]

    HKEY_CURRENT_USER \ Software \ Classes \ Local Settings \ Software \ Microsoft \ Windows \ CurrentVersion \ TrayNotify
  3. Delete the two values namely IconStreams and PastIconsStream
  4. Exit the Registry Editor
  5. Terminate Windows Explorer / Shell cleanly. [Instructions for Windows XP / Windows Vista, Windows 7]

Script to Automate

Here is a VBScript (runs in Windows XP/Vista/7) that can automate the above task for you. Download, unzip and run clear-notification-items.vbs file. It clears Customize Notifications items and restarts Explorer shell automatically.

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Dang, I was too slow! – Moab Apr 3 '11 at 20:47
@Moab: Wild wild west! ;) – Mehper C. Palavuzlar Apr 4 '11 at 6:47

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