EXPERT RESPONSE
What data you need is wholly dependant on what is deemed critical. From a Lotus Domino perspective, names.nsf is the only "necessary" database. Other directories and mission-critical applications should also be considered, as well as key mail files and the like. You will need separately stored server ID files, Notes.ini files and the like, since those do not replicate.
As for the disk activity, there is nothing you can do. Those tasks are extremely disk-intensive, because they are either copying data, querying data, or rearranging it. The only thing you can try is to limit those activities to off-hours via program documents.
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Related information from SearchDomino.com:
Tip: Lotus Notes/Domino replication primer for administrators
Reference Center: Notes/Domino administration
Reference Center: Notes/Domino database backup
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