Squirrels have fuzzy tails.
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I've noticed in a few of my applications that motor controllers (I've seen this happen with RC servos and larger DC motor controllers) that as much as 2.5V can be fed back to my power supply circuits, coming from the microcontroller, through the signal line(s), through the motor controller, and back the power line (5V in all of the applications I've been working with). It's enough power to light up my status LEDs (indicating 5V power) even when there is no source 5V.
I've thought about using diodes (from 5V supply to 5V input to motor controller/servo) to provide reverse current protection, but I'm worried the diode drop might interfere with the onboard logic as the control signals will still be coming from the 5V microcontroller.
My question is 2-fold: should I worry about the diode drop? And if so, is there another way to provide the "one-way valve" effect that I'm looking for?
How did you establish the path of the voltage?
You just claimed that it came "through the signal line(s)" and if it does, they'd need diodes as well.
First, make sure there really is a problem, then establish exactly where it is and whether it... Well, is a problem (i.e. has any ill effects).Then a solution can be selected.
 I was mostly curious about whether this is a common problem (it must be) and how to avoid it.
Thank you for taking the time to look at this and the in-depth reply; this was a great introductory experience to this forum, the atmosphere here seems quite helpful.
When main power is disconnected from the peripheral 5V LDO, but the Arduino PWM lines are still connected to the motor controller, and the motor controller is still connected to the output of the 5V LDO, my 5V power LEDs still light. When either the motor controller is disconnected from the 5V rail or the PWM lines are disconnected from the Arduino, the LEDs turn off (the correct state, as there is no main power to the 5V LDO). Also, I've experimented with the diode installed such that current can only flow from the LDO to the motor controller, and this also shuts off the LEDs.
We can only reply as in-depth as the information allows. The better you describe the problem, the more helpful we can be.
I believe the internet ate my tone:
As for the schematic, hopefully this image (I don't have a formal diagram yet) will help: