As the Good Book Says: The movie starts off with a quote from the Book of Job, to set the theme about the role of God in the universe and how God's way is often incomprehensible to human
Where were you when I laid the foundations of the earth? Tell Me, if you have understanding. Who determined its measurements? Surely you know! Or who stretched the line upon it? To what were its foundations fastened? Or who laid its cornerstone, when the morning stars sang together, and all the sons of God shouted for joy?
Billing Displacement: Sean Penn is billed second but appears in only about five minutes of the film.
Blessed with Suck: Mankind. And yet, at the same time, the film still has a hopeful tone.
Decoy Protagonist: Zig-zagged. Jack's parents (particularly his mother) are the POV characters until the focus switches to Adult Jack who is given several minutes of build-up before the focus abruptly switches back to his mother (who monologues during the Big Bang/Creation sequence), and then finally settles on Young Jack for most of the movie. Then, in the last few minutes, the focus shifts back to Adult Jack, then to the Mother, and finally back to Adult Jack during the final seconds.
Development Hell: Malick began work on a project enigmatically entitled Q before making The Thin Red Line, only for it to come to a halt. Apparently, Malick used Q as a basis for The Tree of Life, which was finally officially announced in 2005, only to have casting issues, gathering up a Dream Team of visual effects artists to achieve his vision, and then work very, very slowly to make everything as good as possible. In short, he's a perfectionist.
Distant Prologue: It begins simply enough, and then the Big Bang happens. Literally.
For the Evulz: One interpretation of Jack breaking into an unoccupied home, then stealing a dress from it and sending it down a river.
Gainax Ending: Once again, you have no idea. Okay, so while everyone in the audience should be pretty certain that the finale involving the heavenly beach, Adult Jack chasing his younger self in the desert, and his mother's prayers are all either a Heroic BSOD or some sort of variation of that, it doesn't make it any less baffling. Audiences will be divided. You'll either feel at one with the universe, or like you're just being shown completely random images.
Gray and Gray Morality: Brad Pitt's character may be a jerk at times, but it's because he cares a bit too much for his kids. Young Jack can be just as jerkish as well, but whether it's from the abuse and expectations of his father, his first time experiencing death and realizing we all don't live forever, or just from general Angst is up to the viewer.
Heaven: At least the ending can be interpreted that way.
I Want My Sons To Be Real Men: Played with. At first, Mr. O'Brian plays this straight, such as trying to teach his kids how to fight. As the movie progresses, he starts to accept that he's doing it more for himself, and promises to be a better father.
Kids Are Cruel: Once Jack's father leaves for a business trip, he and his friends start to drift into crueler acts, like blowing up birds' eggs or tying a frog to a rocket.
Living Prop: Jack has a wife, but all she does in the film is get dressed for work and leave.
Meaningful Funeral: One of the many important events building to Young Jack's loss of innocence.
Metaphysical Place: The heavenly beach, the vast desert Adult Jack wanders through, that weird field with styrofoamy-looking rocks or plants or whatever those are supposed to be. Expect this to pop up a lot.
Mind Screw: Not just the Gainax Ending, but a few brief, but glaringly noticeable shots such as the underwater house shot signifying Jack's birth and one very random scene in which the mother is floating and dancing in the front yard. Why? Because True Art Is Incomprehensible
Mundane Made Awesome: Ye gods. As if the constant Ethereal Choir over family picnics and kids playing wasn't enough, a tense family dinner is played to swift classical music, which may or not have actually been in the scene.
No Name Given: Only Jack is given a name within the story; the other brothers' names and the family surname are only revealed in the credits: R.L. and Steve O'Brien.
Stalking Is Love: Jack gets a crush on a fellow classmate and follows her home. Later he spies on through her house's windows and sees her father yelling at her mother. Lastly, he enters their house while her family's gone.
Stunt Casting: Sean Penn as a guy with about 10-or-less non-consecutive minutes of screen time and barely one line of dialogue in an over-2-hour movie. Penn has gone on record saying that his role in the final cut contributed nothing to the film and served no purpose; he also mentioned that, in light of this, he was at a loss as to why the director didn't cut him out altogether.
Tempting Fate: Kid, if you think that putting your finger in front of a BB gun will result in anything other than pain and misery, your loss.
Averted earlier with Jack's brother being dared to poke a wire into a lamp without the lightbulb. He's initially suspicious, but even after licking his finger and poking it in, still nothing happens.
A specific example: Heath Ledger was originally cast as Mr. O'Brien, and his death put the production into a tailspin before Brad Pitt volunteered to take the part.
Another specific example: The original cut was said to be over 4 hours long, and Adult Jack (Sean Penn) had a much, much larger role. Penn can barely even relate the script he read and the cut they released to be the same movie.
What Happened to the Mouse?: There are many quick visuals and suggestions of bigger stories that are merely glimpsed and then never revisited, including: a man has a seizure on the family's front lawn, and the mother prevents her children from seeing it; a man is arrested as the entire town watches; a house burns down and a young boy, one of the brothers' friends, suffers burns on his head, and more. Also, we never find out which brother died.
Although it's never clarified, from Mr and Mrs O' Brien's reactions to seeing him on the beach coupled with the emphasis on his and Jack's relationship it is presumably the blonde slightly younger brother who kicks the bucket.
World Tree: Despite the title, it's mostly averted.
Although there is an awful lot of shots of trees, many of them positioned so that the tree takes up most of the frame.
Write What You Know: Malick grew up in Waco, Texas which is where the film is set. Like Mr. O'Brien, Malick's father gave up on his aspirations of becoming a musician but played the organ at his church. Also, Malick's brother died (suicide) when he was a young man, much like Jack's brother R.L. His other brother was badly burned in a car accident, which may have inspired the badly burned neighborhood boy.