I think it's important here to not get into a set routine that is supposed to cover every situation. For those that do not feel safe with a loaded chamber, clambering a round should be done as soon as the gun is picked up in response to a possible defensive situation. 911 is also on top of e list, probably #2 behind clambering a round, due to the fact that handling the phone while chambering a round requires three hands! But after that, there are too many variables to pre-determine a response.
Example: A drunken college kid forces my front door open, then stumbles through my living room. Do I arm myself? Of course. Do I shoot immediately? Of course not. I tell him to get out or sit and wait for the red-and-blue lighted taxi to take him to the Iron Bar Motel. He isn't a danger to my life even though he has committed multiple felonies. Now, same front door gets forced open, but standing in front of me is a 275-lb, prison-tattooed, drug abuser who is obviously either high or jonesing for drugs. If I have appropriate distance, he MAY get the courtesy of a warning. But any aggression such as moving towards me or drawing a weapon means we have escalated to a point where shooting may be the only viable alternative.
Warnings or cocking the gun for effect may or may not have an affect on the intruder, but it's important that it not be a fixed item on your list of "To Do's" before you can pull he trigger to effectively defend your life. Warnings are great for diffusing situations that are not clear or that can be handled without a shooting. Warning are much cheaper than a shooting with all of its lawsuits and psychological trauma and should be a tool, just like mace, a baton or other non-lethal solution. But nothing should interfere with your thought process of escalating to the level needed to defend your life. Protecting yourself should always include your sanity and your finances along with your body.
“Malo periculosam, libertatem quam quietam servitutem." (I prefer the tumult of liberty to the quiet of servitude.). Thomas Jefferson
"All that is necessary for the triumph of evil is that good men do nothing."
-Edmund Burke, Loosely translated from Thoughts on the Cause of Present Discontents. (1770)