Maybe one "missing" feature on Zimbra is the support for S/MIME in the webinterface. Of course it's possible to send cyphered and/or signed emails using and email client like Outlook or Thunderbird via Zimbra's server, but I think that being able to sign emails with a x509 digital Id (and/or PGP) it would make it more powerful for environments and business where it's important the "non-repude-on-origin" (or whatever is called in English) and the confidential transmissions of information.
I think that only CommuniGate Pro offers the possibility to cypher and sign emails via a webinterface, and Horde with PGP. If I'm right Scalix doesn't support neither this possibility and I think that it would be a "goal" to offer this option that, everyday, is being more common and valued for customers on many fields (medical, legal, etc.), maybe in the network edition as a professional feature.
It's just a reflection to the "wish list"