Tony has a Wing Chun dummy in his workshop and gives it a few strikes in passing. Robert Downey Jr. is a practitioner of Wing Chun in real life, and it's his fighting style of choice for 'Sherlock Holmes''.
Killian makes an offhand reference to stereotypically eccentric behavior by stage actors. Guy Pearce got his start as a stage actor.
Harley breaks a finger off of Tony's Mark 42 Armor. Tony's narration gets away from him a few times, not too unlike Harry's.
Death by Cameo: Inverted with the AIM mook who gives up and runs away from Tony. He's played by the movie's fight coordinator, Si-Fu Eric Oram. This makes his line, 'Honestly, I hate working here; they are so weird.' even funnier.
Dawson Casting: Downplayed, but Robert Downey Jr. plays the 20-year old Stark during the flashback at the start of the film.
Fake American: English actress Rebecca Hall as American Dr. Maya Hansen, and Australian Guy Pearce as American Aldrich Killian.
God Never Said That: Many of the rumors by sources such as Latino Review that have been attributed to Marvel Studios such as a post-credits scene involving Tony going into space and meeting the Guardians of the Galaxy have been debunked by Kevin Feige himself.
Gandhi appears to have pulled a Face-Heel Turn, and now wants Sherlock Holmes dead for stopping his terrorist organization's operations. And he's still played by a British actor, but this time in-universe.
Looks like Leonardnote Guy Pearce found the solution to his memory condition; Extremis.
I Knew It: Averted but what makes this notable is that the movie managed to keep its twist secret enough to the point where almost no one saw it coming. This is quite an accomplishment considering that films such as The Dark Knight Rises are having their twists correctly guessed before they even came out.
Short Run In Peru: The film was released in theaters in dozens of countries at least a week before the US.
Torch the Franchise and Run: After this film, Robert Downey Jr.'s old contract expired. Unless he chose to sign a new one, he no longer would have to play Iron Man. As such, the film went out of its way to serve as a finale for Tony Stark's character, just in case this was RDJ's swan song: Tony loses the shrapnel in his chest, destroys his armors and seemingly retires from superheroing. All of that said, however, the words "Tony Stark will return" appear on-screen following The Stinger, and he's signed another one (or rather, two more Avengers movies).
A Super Bowl trailer that promised an 'extended look' had Robert Downey Jr. staring at the camera. To be fair, "extensive" and "extended" could be easily confused.
Many elements in the film were Red Herrings that were obviously designed to fool the audience, such as getting someone as high-profiled as Ben Kingsley to play The Mandarin (who's nothing more than a dupe) and the post-credit scene not being an Avengers 2 plug.
Subtler, but the director makes use of the whole 'HUD on Tony's face' thing to keep audiences guessing if Tony's even in the suit.
Early discussion implied Killian was a glorified cameo, and that Guy Pearce was a last-minute addition to the cast. He is, of course, the Big Bad.
As for official Iron Man 3-branded Lego: One of the sets is called "Iron Man vs. the Mandarin: Ultimate Showdown", and features Tony going up against the Mandarin in a weird weapon-covered tank-thing, the obvious implication being that this is a toy recreation of the film's big final battle. That's right, even the toys are deliberately misleading you as to the film's plot! (There's also a set based on the scene where Tony's house gets blown up which includes a Mandarin figure, implying he's flying one of the helicopters.)