I am currently working gutting an old clock and replacing the spring mechanism with a stepper motor. Because of the gear ratio the stepper motor advances 1 step every other second. I am using the "Stepper" routine for my program.
I am wondering how to turn off the motor after it has made its step. The stepper motor with the power applied holds the position of the rotor because this is a clock there is no load to back drive the motor. Turing off the motor winding's will reduce the amount of power that the clock draws, it will also reduce the amount of heat generated.
Use a smaller, lower power stepper motor. Run the motor at a lower voltage, if you don't need much torque you can lower the voltage. Limit the current to the motor to limit heat buildup and limit torque - this is an optin if you are already using a lower voltage.
If using a unipolar motor you can tie the 4 transistors/MOSFETs to 4 Arduino pins and drive the stepper motor using your own code - not that hard to do... look at this thread for a way to do it, just don't use it as an interrupt function - http://arduino.cc/forum/index.php/topic,84809.0.html - Look at the step function and add code at the end of the function to turn all the outputs off before returning.