We crimp APPs to every motor on our robot. We have a standard pigtail length, and zip tie the APPs + pigtails in such a way to provide strain relief.
This makes swapping out failed motors very straightforward, and ensures all our spare motors will always fit, without having to rewire anything.
We do the same with our sensors by putting PWM connectors on a standard pigtail length.
At the speed controller, we do not use APPs. Instead we use standard crimp quick-disconnects in combination with these:
http://www.digikey.ca/product-search...yWords=42095-1
They make swapping out failed speed controllers a breeze - but we also usually mount one spare speed controller of each type on the board. These disconnects also make swapping a motor over to a spare motor controller very easy. We keep a few quick disconnect extension cables handy - male on one end, female on the other. In a pinch we can move a motor from a failed motor controller to the spare, and make a quick code change.
After doing this for a few years, it also makes prototyping go smoother, because all your motors and sensors a plug and play!