Once upon a time I designed a versioning system for an object graph. It was for an application framework that was meant to be designed in an IDE, and didn't have source code, per se (it did have little snippets of code). But designing it around graph deltas, rather than versions, was always the right thing to do: that much was self-evident.

Even as I use svn today, I turn almost all my work into patches. For every bug I fix and every feature iteration, it gets turned into a patch. That way it's usually pretty easy if I have to apply it to an older branch for a hotfix or whatnot.