[Mark McLeod]

Pretty much anything you think should be set to zero for safety sake.
Here's the danger.
If your robot gets Disabled while moving drive base or mechanisms, will that be overridden immediately if you startup again in Autonomous or in Teleop?
Otherwise, when you Enable again the robot will continue trying to do what it was at the time it was Disabled, even though Autonomous will start over at the beginning again.

If you are following the Safety vi feeding schedule in both Autonomous and Teleop, then it probably doesn't matter for drive motors, but it still might for secondary motors.
For most of us, Teleop will immediate set most motor outputs, so that might not be a problem.
Autonomous is the more dangerous issue. If you don't bother to command a motor until later on in Autonomous, then you've got a problem.

P.S. There are also issues with feedback mechanisms that try harder and harder to force the robot somewhere, until suddenly the robot is Enabled again, but the feedback is by now commanding warp speed, because nothing slower was working while Disabled.