Currently rsnapshot, however I'm considering a move to duplicity (perhaps via http://chrispoole.com/project/horcrux/ ) in order to get the additional feature of offsite encrypted backups
I'm pretty sure that he means for duplicity.
I'd imagine that this comes into play when duplicity puts everything into a single file archive (tar IIRC).
I haven't seen any issues with rsnapshot in regards to this.