One of the biggest topics on the news currently is about the disappearance of the Malaysian airliner. I seem to vaguely recall movies with this theme, but don’t remember titles, plots and if they were any good.
Anyone remember?
There are far more about disasters on board, not so many about simple disappearances.
A few that come to mind:
The Flight That Disappeared (duh)
Millennium
The Disappearance of Flight 412
If you’re willing to include TV, there was the pilot episode of “Lost”, and an episode of “Banacek” titled “Fly Me — If You Can Find Me”.
There are others about military or exploration flights, but you’re asking about airliners.
If any were good? Not by conventional standards, but for those of us who love this stuff, they all were. 
Technically, the aircraft in the film The Langoliers based upon the Stephen King story, “disappears.”
I came in here to post this! I thought that was a pretty obscure film.
This one is obscure (I’ve only seen it on a Spanish channel): Air Force One is Down. It was actually taken over by remote control by tech-savvy Croatian terrorists, who landed it on a secret field in such a way as to look like it crashed in the Mediterranean, kidnapped the President (Linda Hamilton can still get work), had the plane take off, let the crew wake up from the sleeping gas, and released control so they could finish the flight.
In Airport 77, the plane technically disappeared underwater, but it was still known where it was.
A couple more:
Five Came Back - it’s a little jarring to see Lucille Ball in a disaster/survival film, but fun.
In Her Line of Fire, featuring Air Force Two for a change.
There are a few Twilight Zones that feature similar themes:
“And When the Sky Was Opened” - about astronauts, but still a disappearance.
“The Last Flight” - a British WWI pilot disappears & lands 42 years later.
“King Nine Will Not Return” - a WWII bomber.
“The Odyssey of Flight 33” - from the passengers’ point of view.
“The Arrival” - a plane lands without pilots, passengers, or luggage.