As a drummer, I prefer the bottom head on, since that is where the majority of the tone, resonance and depth comes from (the top head is primarily attack).
As an engineer, I find it can often be easier to record drums with only batter head on - and when close mic'ing the majority of the recorded sound is coming from the top head anyway (eq and reverb can be used to add depth).
If there are room mic's, I prefer the bottom head to be on to add to the room ambiance and overall drum resonance, but if there are only close mic's, it is more a matter of what the song needs and what provides the best sound.