i am not sure if it is the correct solution, but it seems, whitelisting
did help!

after issuing the following commands:

    gsettings set com.canonical.Unity.Panel systray-whitelist
"['JavaEmbeddedFrame', 'Wine', 'Skype', 'Dropbox', 'Cryptkeeper']"

    setsid unity

... the beloved cryptkeeper-icon appears in the top-bar and everything
is working as expected :)

the second command (re)starts  unity in a new (terminal-)session so it
will not be ended if you close the terminal window, you could also
entering "unity" to the <alt><F2> dialog or you could logout and back in
to make the changes take effect.

using cryptkeeper 0.9.4-1ubuntu1 (natty)

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https://bugs.launchpad.net/bugs/689071

Title:
  Crtypkeeper does not add to Unity Launcher

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