The title is taken from Edwin Starr's song "War." Which is one of the four horsemen featured in this episode.
When Ellen returns from looking for Jo, she knocks on the hideout 9 times, using Morse Code, consisting of 3 fast knocks, 3 slow knocks and finally 3 fast knocks. In Morse Code this spells out S.O.S, which is a mayday emergency procedure word for requiring help or Save Our Souls.
When asked if these problems come from space, Dean comments that this "is not X-Files." Actor Steven Williams (Rufus) is best known for playing Mr. X in The X-Files (1993) as well as roles The Blues Brothers (1980) in and 21 Jump Street (1987).
When Castiel first gets to the hospital and tells Sam and Dean that they are hidden from him, Misha Collins uses his real voice, which is much higher than his "Cas" voice.