Here is how I do it, as recently as last month, and I have never had a problem.
My unloaded gun and unloaded magazines go inside of a steel lockbox for which only I have the key. This box goes inside my suitcase. I also pack my ammo in its factory box, and put it inside my suitcase, but not in the lockbox containing the gun.
At the check-in counter I tell the agent "I want to declare an unloaded handgun." The agent then gives me the declaration card to sign, which I then place in the suitcase, adjacent to the lockbox. The agent sometimes wants to see the lockbox, but not always. It has been years since I have been asked to open the lockbox to show that the gun is unloaded.
Then, after securing my suitcase with a TSA lock (remember, the gun is in a steel lockbox for which only I have a key, placed inside that suitcase), and depending upon which airport, one of two things happens: 1) The airline agent takes my suitcase, but asks me to hang around for about 10 minutes to ensure clearance, or 2) I am escorted to the TSA baggage screening area where they screen and give me the thumbs up. I then head to security and my gate.
Sometimes, but not always, my suitcase receives a "Special Handling" tag. I like when this happens, since more often than not my bag doesn't come down the conveyor at my destination, but is walked over to me where the baggage handler checks my claim check. Note that the bag isn't marked "GUN INSIDE!", just "Special Handling". The first time this happened i wondered if "Special Handling" wasn't going to result in "Special Pilfering", but this has never been the case.
Note that traveling with a handgun is much easier now than it was prior to 9/11 since it appears that folks (other than the idiot in the video) are much more aware of the proper process.