Rsync all the way.
rsync of course
I like both GoodSync and JFileSync
BEYOND COMPARE.
Yes, It gives Automatic+Manual control simultaneously. Just try it.
CopyTo
I've used SyncToy 2.0 forever to backup critical folders to external HD's... works like a champ!
WIN - I have used SyncToy for a long time - free - but Beyond Compare has many more functions - its great - worth the money
UNIX - rsync
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I still say Unison wins, simply for it's great scriptability and pure power. Also, since it's terminal driven (there is a GUI), it can be run through SSH to keep everything secure; it also has the ability to contantly sync (in instances where needed) as well as many other cool features.
Did I mention completely cross-platform?