@MatthewSteen, I assume you only put in same zone when they are similar adjacent spaces. There may be many times you don't want them in the same zone either because they are not adjacent, or they have very different (internal or external) loads.

I was thinking to not assigning the space to a HVAC system.

@David Goldwasser - I see your point but have not typically considered the inter-space heat transfer to be significant enough in a commercial (internal load driven) building to warrant that level of detail. It's a simplification but one I think is reasonable. If I were doing an existing building model I would probably take these small details into consideration.

@obuchely - that will work. According to EnergyPlus a zone is considered "conditioned" if it has a piece of equipment assigned to it (Fan:ZoneExhaust, ZoneHVACEquipment:*, etc.) just be mindful that each space must (I think) be assigned to a thermal zone or it will cause an EnergyPlus error.