Ned Batchelder has come up with an interesting hack for increasing the granularity of his code coverage testing. It involves modifying the code object associated with the code being modified: specifically, the co_lnotab member contains a starting line number followed by a sequence of (code offset, line number delta) pairs.
Ned's technique involves rewriting the member so that each bytecode appears to be on a single line on its own. While this allows him to ensure that all bytecodes are exercised, he hasn't yet ironed out the quirks in how to use that to present coverage information (which is hardly surprising, since most Python programmers could care less about the structure of their bytecode).
It seems to me, however, that by mapping the modified co_lnotab back to the original you could at least flag lines whose code isn't 100% covered by your tests, and this is surely valuable information. Ned's already thought of this, and includes the throwaway remark "The original line number information is lost. It would have to be stored off to the side to make this useful" towards the end of his blog entry.
So I believe we can expect coverage.py to start producing even more useful information soon.