To run PID Autotune in Marlin and other firmares, run the following gcode with the nozzle cold:

M303 E0 S200 C8

This will heat the first nozzle (E0), and cycle around the target temperature 8 times (C8) at the given temperature (S200) and return values for P I and D. An example from http://www.soliwiki.com/PID_tuning is:

bias: 92 d: 92 min: 196.56 max: 203.75
Ku: 32.59 Tu: 54.92
Clasic PID
Kp: 19.56
Ki: 0.71
Kd: 134.26
PID Autotune finished ! Place the Kp, Ki and Kd constants in the configuration.h

http://reprap.org/wiki/PID_Tuning
http://www.soliwiki.com/PID_tuning