Is there a version of ExMerge capable of extracting mailboxes larger than 2GB (Exchange 2003 and 2007)?

Hi, No, ExMerge uses ANSI formated PST which has limitation of 2GB. You can use Export-Mailbox/Import-Mailbox cmdlets of Exchange 2007 SP1 if you have coexistence environment which handles both ANSI & Unicode formatted PSTs. How to Export and Import mailboxes to PST files in Exchange 2007 SP1 http://msexchangeteam.com/archive/2007/04/13/437745.aspx

What about for 2003

Hello, Well, in coexistence (Exchange 2003 + Exchange 2007) environment you can still use Import-Mailbox/Export-Mailbox on Exchange 2003 mailboxes. But in pure Exchange 2003 environment you need to follow some workaround available in below KB. http://support.microsoft.com/default.aspx/kb/916085