ZFS solves the hard-link problem spectacularly well (and adds a whole bunch of data-integrity verification on top of that) with snapshots.

What I don't like about that solution is it can't dedupe (ZFS dedupe just ultimately doesn't work very well). Hence my interest (and if anyone checks my post history, my constant spruiking of) bup - which does efficient dedupe and output of git pack-files. Stick that on a ZFS volume with snapshots, and you've got block-level checksummed, versioned and deduplicated backups.

What it's all missing of course, is a pleasant interface to use it with (one which doesn't fallback to the thing I see way too often in a lot of these scripts "don't worry, we're just going to stat your entire filesystem every 20 minutes).