To discuss the best whole building energy modeling software, we should consider: ASHRAE Std 140 approval, power, flexibility, feature-rich, learning curve, existing audience, reports, customization, and maybe a few more things. You might care about cost too. The only free software on the list is eQUEST.
That narrows the discussion of best software down to a few software packages:
- EnergyPlus+OpenStudio+Trimble