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>>Have you looked into Publishing the main database and Subscribing at the remote sites?
>
>Wouldn't this only be one way replication?

No. Look at Merge Replication in SQL Server 2005.

>Could only conditional data be replicated to each subscriber (only that users data for example)? I should also mention that there will be several thousand client installations.

Yes. I'm not sure of the administrative practicality if thousands of clients each have unique datasets.