"wantonly destroying cities, towns, villages, or any object not warranted by military necessity" is a war crime.

A plane would be such an object.

"murdering, mistreating, or deporting civilian residents of an occupied territory to slave labor camps" is a war crime.

Passengers of an aircraft traversing an occupied territory could be construed as civilian residents.

http://en.wikipedia.org/wiki/War_crime

"Murder, extermination, enslavement, deportation, and other inhumane acts committed against any civilian population, before or during the war..." is a crime against humanity.

http://en.wikipedia.org/wiki/Crimes_against_humanity