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Once you compress the image, it shouldn't matter if you included unused space or not.
duplicity is the standard backup tool, but it doesn't sound like it's what you're after. It would be a lot more space efficient though
cyclotron3k
Cheers. I'd favour a disk image over copying files (easier to restore and I seem to remember stuff about rsync not necessarily playing nicely with NTFS drives). dd could be an option unless anyone has any better suggestions. Something that produces images on the basis of space used rather than SD card size would be good.
Although I assume this will founder where I often do with problems on writing to a samba share.