If you are looking to get into a high powered, academic, publishing machine, a letter from a commmunity pod MAY not be looked at as highly. If you are looking to go to one of the less research oriented academic programs, or a community program, I think a letter from a community pod that really knows you would be great.
You could try to submit the non-academic letter to programs that will likely not care and try to find an academic letter for those big guns, or just go for it and put in the letter from the guy that knows you best. I would put in the letter from the community pod for every program, but I have made it clear in the past that I don't intend to play the game. I say screw any arrogant PD that thinks only academic pods write letters worth reading.
