In my experience, it's just a matter of iteration. Put your data and code wherever you think they go. Chances are, you'll be wrong anyway. But once you get a better idea of exactly how things are going to shape up, you're in a much better position to make these kinds of guesses.
As far as extension sources, we have a Code directory under trunk that contains a directory for python and a directory for various other languages. Personally, I'm more inclined to try putting any extension code into its own repository next time around.
With that said, I go back to my initial point: don't make too big a deal out of it. Put it somewhere that seems to work for you. If you find something that doesn't work, it can (and should) be changed.
