As part of the company name change, the email domain has changed from domainone.com to domaintwo.com.

What's the best way to do it with zimbra (open source)?

A quick bandaid I can think is to create the new domaintwo.com as an alias and forward to email to the old domainone.com:
http://www.zimbra.com/forums/showthread.php?t=847

pros: people can still use the old username/password to login; have access to all their old emails; minimal changes to the system.
cons: old domain is still being used.

A better solution: create the new domaintwo.com domain; somehow import all users/data from domainone to domaintwo (how?); delete the old domainone; create domainone as an alias to forward all incomings to domaintwo; eventually delete domainone when nobody is using domainone in the future.