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I love this question and am looking forward to others answers, here are a few ways we check our models:
We take the overall EUI of the building and compare it to CBECS data and other information we have on whether this is a realistic number. It is either miles out or in the right area.
We take the EUI of individual outputs, say, heating, cooling, fans etc... and we look and compare those EUIs to other projects we have done and use judgement as to whether this is reasonable for the climate and what we know about the building.
We look at the unmet load hours and which zones aren't meeting their loads.
We take a look at how the energy flows through the system, so in EnergyPlus we can do this by checking the nodes at each point in the AHU and in the zones and in the plants. From this you can check to see that all your components are working correctly. There is more on this on the question MattSteen has mentioned above.
From there it is a question of finding the issues and checking your inputs from the issues that have come out rerunning and reanalysing.