Probably impossible to list all, but here are really harmful if you are moving it to other server:
- by default it creates 80g (sparse) file for ldap db - if you try to do backup/restore using procedure from their site you are screwed (instead use normal tar with S to support sparse files)
- for some brilliant reason they are saving numeric uid of zimbra user in config file, so again if you backup/restore installation and uids do not match on new machine you will end up with bunch of permission denied errors in log files (local config file is in conf/localconfig.xml)
Recommendation - stay away from zimbra if you can.