First of all, there is a new notes.ini setting: ADMINP_EXCHANGE_ALL_UNREAD_MARKS=1. This new setting is available for Domino 6.5.6, 7.0.3, and 8.0. It is detailed in Technote 1245043. This setting will exchange all unread marks in new replicas created via the Administration Process (instead of only the default 90 days worth). Also, it requires that only the source server be running the fixed version of the server code.
Secondly is a new option in the Create Replica(s) dialog box. As depicted in the graphic below, there is a new option to "Exchange Unread marks on replication":
This works very similarly to the notes.ini setting described above. If the source server is at Domino 8.0*, then the Administration Process will "attempt to match all of the unread marks from the source database with the target database."
* - I had hoped that this would work with Domino 6.5.6 or 7.0.3 servers like the notes.ini setting, but it does not. The source server and Administrator Client have to both be at 8.0 or higher.