On a Citrix or Terminal Server you will want to disable autoupdate notifications of the flash player.
This can be done by creating a file mm.cfg in the folder where the flash ActiveX control is installed (normally C:\Windows\System32\Macromed\Flash).
Place the following line in this file (with a text editor like Notepad):
AutoUpdateDisable=1Be sure to save the file with UTF-8 encoding, this can be selected in the Save As dialog in Notepad:

Ofcourse you are aware that only certain Flash versions are supported (and optimized) in Citrix? At this time these versions are: 7a, 8, 8b, 9, 9c, and 9d.
I found that the filename should be mms.cfg instead of mm.cfg. After putting the file in the correct directory on my terminal servers (W2k8 R2), the notification is still popping up...