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0e1f616
(Get the code!)
I understand Mark's approach, at least for apps which aren't included in the repos, e.g. Truecrypt. Canonical has never claimed to support them.
For business users the LTS releases are recommended, anyway. With Ubuntu 12.04 they can still use systray for another 4 years. Then Ubuntu with Unity is either a major OS or legacy itself. In both cases we won't need systray in Unity anymore. If it's then still in today's market position, the removal of systray won't have had a big effect. So it's not worth to argue about it.
But I also agree with Jason. Users expect apps from the repos to work, especially those which are installed by default. To include apps from Debian makes only sense, if they work. I'm not sure, but isn't e.g. Vino included in the default installation of Ubuntu and needs whitelisting to work properly?