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As John indicated, Interoperability between operating systems and versions is not a problem for Domino.
If you could get the Domino versions synchronised, then you could move towards merging the domain, this would get you to an "option 1" scenario. I would not recommend this until all the systems were within a similar code stream (eg: 8.*).
After licensing and hardware considerations, I would be pushing for the organisation on Notes 5 to upgrade as soon as possible - those poor folks are having an extremely outdated user experience. Even without upgrading you can get this underway.
To get things started, if you are the "God Admin", I would get you (or your Notes Admin's ID) cross-certified with company* as soon as possible. Once that's done, ensure the other Domains include a LocalDomainAdmins group, and include your name in that group. Once you've done that - the rest becomes fairly straight forward and easy to manage.
Create the Cross-Certificates between the Organisations (it's the Org's, not the Domains that have "Trust") in both directions, ie: Company1-Company2, Company1-Company3, Company2-Company1, etc.
Create "Adjacent" Domain Documents within the individual Domains (company1 needs DD for company2 and company3)
Create Connection Documents to map the Domain documents above (eg: server1-server2, Server1-server3...)
In each Domain, add the "foreign" servers to the "OtherDomainServers" groups.
Ensure that each Domino Directories ACL contains the OtherDomainServers group and is set to at least "Reader"
Create a replica for each of the Adjacent Domain's Domino Directories on the server (server1 should have replica's for Company2 and Company3). Ensure you set the filename on the replica's properly, eg: on Server1 you already have names.nsf, therefore the replica's from the other domains should be namesc2.nsf and namesc3.nsf. Be mindful of the OS File name conventions here.
Use the connection documents created earlier to set the replication schedule for the Domino Directories.
On the Domino 8 and 6 systems, configure a Directory catalog, On the Domino 5 system - I would recommend using Directory Assistance instead.
Once the Catalog/DA is configured, a restart of the servers should see the users able to use any name immediately from any other Domain in an Address or Security field.
That should be it, Generate The Trust, Establish the connectivity and update schedule, Use the local replica's to configure Address options.
The Catalog/DA allows the Name look-ups; the Cross-Certs, Domain Docs and Connection Docs ensure native (NRPC) connectivity between the servers. Not only will you be able to do name look-ups, users will be able to send Native Email, Calendar Invites, Links, etc between Domains, and even do a "free-time" look-up for a meeting with a user in another Domain.
Hope this helps,
Mat
Feedback response number MNEN7X4PWL created by ~Justin Zekboositerynds on 10/23/2009
Configuring the Domains to communicate
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. . . . . . Configuring the Domains to communic... (~John Eklupulji... 23.Oct.09) 
