Wyldstyle's introduction, feats of skill, and role in rescuing the prophesied hero is comparable to that of Trinity of The Matrix. The Think Tank is similar in concept to the cells where the Machines put the humans to use them as living batteries. There's also Emmet finally grasping the rules of his universe in the climax.
The location for the Lego Castle theme in this world is referred to as "Middle Zealand".
BIONICLE, LEGO Speed Racer, Fabuland and LEGO Friends get a reference in a blink-and-you'll-miss-it montage explained by Wyldstyle. Some see it as a Take That against these lines because Wyldstyle doesn't deem them worth mentioning by name.
At Cloud Cuckooland, Batman is annoyed by a clown and a man in a dino suit. So the Joker and Killer Croc, essentially.
During the attack on Cloud Cuckooland, a unicorn runs by on fire. The same thing is witnessed during the climax of Avatar.
The destruction of Cloudcuckooland is also similar to the terrorist attack on the good side of Imaginationland from South Park's Imaginationland trilogy.
Emmet's fall down the black hole marking the edge of the universe resembles the Stargate sequence from 2001: A Space Odyssey. Additionally, Lord Business refers to his flying headquarters as a "black monolith".
An extremely subtle reference is slipped in during the climax, shouting out to BrickFilm community. One of the first major BrickFilms (stop-motion movies made out of Lego, no doubt a big inspiration for the film) was ''The Magic Portal'', made sometime in the late 80s. Now, look at the tube that Finn uses to send Emmet back into the Lego world at the end: what's it called? The Magic Portal.
Johnny Thunder's cameo role includes two jokes referencing his Indiana Jones Expy status: An Indy Hat Roll through the portal when Wyldstyle explains how the Master Builders escaped Lord Business's forces and running from a golf ball during the assault on Cloud Cuckooland.
A dolphin chirp is thrown in when Emmet is being booed by the Master Builders (specifically, from a shark that someone threw at him). Dolphins were a Running Gag in Clone High.
The Cleopatra mini-fig waves pom poms when the NBA all-stars are fighting Bad Cop and the micromanagers. Cleo in Clone High was a cheerleader.
The DVD-exclusive short Michelangelo and Lincoln: History Cops has definite shades of Black and Tan from the episode "Film Fest: Tears of a Clone".
The term "Master Builder" is a title given to employees of LEGO whose job entails helping to design new sets and also building large, complex statues out of LEGO bricks, the kind that are commonly displayed at LEGO theme parks and retail stores.