I have a Windows Server at a data center and an EC2 Windows Server running in the cloud. In the *Nix world I know the answer to sync these would be rsync. What are some good options for Windows? Is FTP over SSL the only choice here? What programs are good for syncing thousands of files over FTP? Robocopy?
How about rsync? I've used this particular Windows rsync distribution with great success.
There is a "friendly" rsync distribution for Windows, DeltaCopy, but I can't say much about it because I've never used it.
Obviously, you'll need to wrap the traffic in encryption, but either SSH or a VPN can take care of that for you.
For a solution you can automate yourself or run on-demand, robocopy can do mirroring similar to rsync (you'll need to have one of the directories available as a shared directory, first, though).
For a more automated solution, you might want to look into DFS Replication. Once setup, it's fairly automatic in syncing any changes.
rsync or any of its front-end that suits your needs is good, as for the encryption you can use putty to create an ssh tunnel between the two hosts