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It will depend on what you want to get out of your simulation, what are you trying to find out? once you have answered that question for yourself the next question is what aspects of the building affect my question. So if you want to know what the annual energy use is per dorm room, rather than for the whole building, or you want to do a simulation for LEED, you would want to zone with the room in mind rather than the whole building or the LEED baseline systems. In general though there are three questions I ask myself. I start with all the rooms as individual spaces then I ask

1. Do these rooms have the same orientation (do all the windows face south, north etc..),
2. Do these rooms have the same occupancy type (ie, corridor, dorm room, bathroom, kitchen)
3. and are the feed by the same AHU and have the same zone conditioning. If the answer is yes to all three of these questions then the two rooms can be in the same thermal zone.

Again depending on what you want to get out of your simulation you might want to ask yourself slightly different questions.