If you think you'll be copying *lots* of tiny files (e.g. Word documents with no graphics), then connecting the drives (if possible) internally via SATA will get the best performance, unless you'll sacrifice tonnes of time by opening up your computer to connect each drive.
If you're expecting much larger files (photos, music, video), then a USB 3.0 enclosure will be the easiest in general to use and the latency penalty incurred by USB compared to SATA is unlikely to make much difference, plus the convenience of not having to open your computer. I suppose there's also a question of how many drives you'll want to connect up.
There's also a question of what technology drives you'll be connecting; USB 3.0 SATA enclosures are commonplace. I've got a ICY BOX brand docking bay that allows 2.5" IDE, 3.5" IDE or SATA drives to be connected. Such a docking bay would be much less of a pain than getting a say a 2.5" to 3.5" IDE adapter.
In terms of software I normally use robocopy that comes with Windows. The syntax I typically use is:
robocopy source destination /MIR /R:0 /XJ
/MIR mirrors the file/folder structure of the source to the destination. /R:0 specifies the number of times robocopy should attempt to transfer a file if it throws an error the first time. /XJ excludes NTFS junctions (which are commonplace in =>Vista user profiles). Robocopy maintains file modify dates which can be useful.