I absolutely love your plugin. You can directly pinpoint the sources of query problems.
get_header, it would show me all the queries happened during the
get_header call. This shouldn't be that hard to implement, just a couple of
indexOf calls to the existing function paths. It would be extremely useful and much easier to extract and pinpoint the problems. It could be implemented to include functions and exclude them as well.
Other than that, mighty fine job. Couple more enhancements and I'll be off to your Debug Objects plugin to try and speed PHP part. Also XDebug might be worth a shot.