I never make decisions that leaves the damage up to random. Then it might hit my science or tech.
So I never push the engines past their limits and always avoid possible danger.
"Don't shut down" and "fly blind" used to be my go-to options because they give the lower damage, but I don't fly blind anymore after my culture got messed up over it. That costs a lot of points.
(For the same reason, damaged landing gear is awful; it does damage in several places and you cannot control where...)