NDMPCopy is a little bit creaky but allows you to control explicitly which directories get copied. It's very useful. When I say it's a bit creaky I mean I've observed some strange and uneven behaviours from it performance wise. It's never threatened our data though and so we still use it without qualms.
We've also used the prototype technology Dave alluded to and that goes like the proverbial off a shovel! I think we were seeing 20+GB/hr between a F330 and an F520. It makes a full copy of a filer (ie we had to be careful to boot with the right OS floppy and such, one of the few times you have to care which CPU you're using) no more, no less.
NDMPCopy has gone as fast as 2.5MB here, over FDDI, the prototype software boosted that to almost 5MB/s and we basically had a full filer copy in an hour and a half!
Sorry this mail isn't very timely, but I hope it's useful to someone.