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I would have to say it depends on the algorithms used. Most likely, disk compression is light-weight as it has to balance space & performance concerns. Backup programs, OTOH, can have higher levels of compression that take correspondingly higher amounts of CPU and longer run times. You will most likely get the best compression using the backup program. Either way, you do want to do compression regardless of source (OS or backup program). Most USB drives top out at under 40MB/s transfer rate while the drives themselves can sustain 60+. The USB interface is the bottleneck and the only way to minimize that is to shrink the amount of data. Compression, obviously, does that.
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