Most modern OSen should have a capable fs abstraction layer, like VFS, which should remove the client from having to know too much about the underlying file system, I would assume. Plus, rsync can do it, as long as you aren't using the --whole-file option.
-- nick The quick answer is that it's too hard. In order to do an in-file incremental, you'd have to have intimate knowledge of the each kind of filesystem structure (ufs, vxfs, ext, ext3, etc). By doing it at the file level, rather than the block level, the OS takes care of all that for you.
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