[iggldiggl]

The ideal measurement would be to get as good a model of day-to-day passenger flows as possible, then simulate the journey times based on both the nominal timetable, and the "actually-ran" timetable in order to also quantify the effects of missed connections.

I think the Swiss actually do something like this, whereas in Germany they've only comparatively recently started doing it, too, and even then I think they're currently only looking at long distance trains, so connections to/from regional trains don't count (and never mind local public transport).