Rob Tiffany has given the Windows Mobile development community a Christmas present - 12 million rows syncing an hour on his test rack. The interesting part of the whole thing is that this is using off the shelf computers.
By adding in some tricked out hardware might overcome some of the I/O bound problems. This includes using SAN or solid state drives on the SQL boxes. And using RAM drives on the IIS boxes. Merge/Replication IIS process creates a lot of temp files so using RAM drives would should give a boost to performance.
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