[to3m]

If the measurements are all over the place, why not take the fastest? The average is no good, because it'll be influenced by the times it wasn't running as fast as possible.

I don't myself lose much sleep over worrying about the times it runs faster than possible.

[fnord123]

I agree with this sentiment. Any time worse than the fastest is due to noise in the system (schedulers etc). So the fastest is the lowest noise run.

Of course, as I said in another comment it depends what you want to do with the measurement. If you plan to edit how long a run will take on an existing system, then you need to accept the noise and use the mean (or median).