What is a good rule of thumb for practical minimum design duty cycle for a PWM DC motor controller?
Let me preface my answer with a disclaimer:  All of my experience PWM'ing motors is with speed control of cooling fans.  Your application will certainly differ, at least a little bit.

The way I find the minimum duty cycle, I look for the minimum that will allow the motor to start spinning.  With standard muffin fans, this is about 40%.  Then I add a small margin just to be safe.  I find this by applying 0% duty cycle and slowly ramping it up until the motor starts spinning.

This startup power is higher than the amount of power required to keep the motor spinning once it has already spun up.  With fans, this is somewhere in the 20-30% range.  In other words, if I wanted to spin a fan really slow, I would have to apply 40% to get it moving and then I could back down to 20-30%.

Normally, just to be safe, I do not go below the startup power.  That way I can be sure that the motor is spinning, although it does limit the minimum speed that I can do.  

There are problems with this, however.  Many things can affect the startup power requirements.  Temperature, motor loading, age, dust, different motor lots, etc.  You have to take all this into account, and built in some power margin.  

Alternatively, you have to monitor your motor through a tachometer or something similar.  Then have some motor control software do the appropriate thing if the motor is spinning too fast or too slow.  Good motor control software will automatically take into account the startup power and other things.  

If you don't want to write motor control software then you have little choice but to empirically measure what the startup power requirement is for your system and then add some more for margin.  And hope that you added enough.