Hi,
Actually the correct answer (for bottling) is the temperature of the beer when you bottle it. You see the beer when you bottle it already has some CO2 left in it from the fermentation process. Knowing the temperature at bottling gives you the CO2 content to start with and lets the program estimate the amount needed to reach your target level.
For kegging it is different - you want to use the temperature you are going to store/serve the beer at since that determines how much pressure is needed.
Cheers!
Brad