I have been a Zimbra user and user admin for two years now and have found Zimbra to be somewhate lacking for a heavy user.
In my case our companies voicemail and general email is filtered to folders which I share to appropriate staff. I am currently using around 200 folders and nearly an equivalent number of filters to sort the influx of email.
Folders are my main point of issue.
-folders need a confirmation box to confim a move (it is so easy to drag and drop a folder somewhere and have no idea where it landed)
-filter management, if you move a folder your filters will not reflect this move (seems like a large hole to me, I recently had to redo 30 plus filters because I was trying to organze)
I will post more as I think of them and have time.