Prior to moving to Simplify3D I would regularly run the PID autotune command (
http://reprap.org/wiki/PID_Tuning) for common temperatures and apply them as needed. It would awesome if 1) PID tuning was exposed in software & 2) the correct values were automatically applied. I think 2) will depend on the hardware you have as the values might need to be set in firmware or just prepended in gcode.