In the Ten Commandments is the command "Honor your father and your mother." That on one hand should not apply when the parents are obviously "off".  They can not command one to sin or neglect a positive command. Yet there is a certain degree that this command sinks into irrelevance. People have almost no idea that they ought to listen to their parents unless they receive confirmation from some other source.

To me it seems that the Torah is saying one must listen to his or her parents unless there is some compelling reason otherwise.  

Yu can see this in most of the Rishonim also that deal with this command like the Rav of Bartenura right there is the Mishna in Kidushin which deals with this commandment.

But clearly the Torah does set limits. We see in the end of Deuteronomy that Moses praised the tribe of Levi for the incident of teh Golden Cal where the tribe of Levi actually killed their own parents when they discovered that they were among the idol worshipers.