Fridge Horror: At one point in A Million Suns, a group of people on Godspeed speculate that someone else could do a better job running things than Elder, giving serious thought to kicking him out of power in favor of another person. One of the names thrown out as a potential candidate? Luther. Who stirs up riots just because he can, who has raped women and tried to rape Amy, and who was very good at hiding his behavior from the public in general. Imagine what things would have been like if he had been put in charge...
Some of the musical sequences are... odder than the others.
The only reason for 'Being For The Benefit of Mr. Kite' is Eddie Izzard. Oh, and to illustrate what happens when you drop acid.
Around the time Max gets enlisted, the plot takes a backseat. It's easier to think of the movie as a series of connected music videos than a story.
The "Let It Be" sequence has nothing else to do with the rest of the film. Aside from Jojo (who never brings it up or seems affected by it afterward) the people in it are never identified, it has no bearing on the plot, and leaves no impact on any of the characters.
Ho Yay: "I Want You (She's So Heavy)" might just be the most homoerotic scene in any movie ever. The army recruiters get awfully handsy while singing a song originally about sexual obsession and lust to a bunch of half-naked young men, as Prudence gayngstfully sings about her own obsession with Sadie.
Jude and Max are very close throughout the film.
Especially if you listen to the soundtrack version of "With A Little Help From My Friends." It's a duet.
The little boy's funeral. Buckets. All of "Let It Be".
Uncanny Valley: The recruiting officers in the "She's So Heavy" sequence; they look human, but their identical uniforms and stiff, precise movements are complemented by the fact that they all have unnaturally massive Lantern Jaws of Justice that make them all appear like identical living mannequins.
The Woobie: Everyone, but special mention goes to Prudence.