During the river chase in the second level, Batman hangs from a rope ladder with sharks nipping at his heels. If only he had some Bat-Shark Repellent.
When being taken away by the police the first time around, Joker says, "Watch the suit, boys!" - his first line in Batman: Arkham Asylum.
Lex Luthor consoles Joker about the prospect of Batman being killed by guessing that Robin would probably put on the Batsuit in his place, as in the Battle For the Cowl comic storyline.
And Joker replies that it wouldn't be the same, which is exactly the problem he had in the comics.
In the Amusement Mile section of Gotham City, you can find a slide attraction called the Helter Skelter. (This may not count because that's what that sort of slide is called in the UK, hence the name of the Beatles' song in the first place.)
In Lego Marvel Super Heroes, a police box can be seen as you travel through the Bifrost.
An achievement for using Hulk's special move on Loki is titled "Puny God", said special move is also downright similar. Additionally, the achievement for collecting one billion studs is "Billionaire Philanthropist", and the achievement for Hulking Out 50 times is "I'm Always Angry!". The punch Hulk gives to Goblin looks familiar...
The achievement for hundred-percenting the game is "You Win a No-Prize!"
Having Magneto drive the Magneto-mobile to the Baxter Building will unlock the "Menace of Magneto" achievement. Menace of Magneto was the name of the fantastic four cartoon episode that introduced the vehicle.
In the X-Men level, the trophy awarded for completing it is Juggernauts and Crosses. Especially since the main series deals about racism as a whole.
When traveling to meet up with Thor to go to Asgard, Johnny mentions that there's something about the rainbow bridge that makes him want to race on it.
During the mid-credits scene, Black Panther leaps in front of the sun and his silhouette makes a very familiar symbol...
LEGO The Hobbit includes several references to The Lord of the Rings (books and movies). The "Po-tay-to" is a quest item, for example, and there are several quotes and LOTR characters that have no relevance to The Hobbit.
In the trailer for Lego Batman 3: Beyond Gotham the rest of the Justice League are giving their thoughts on Batman's new space suit, Wonder Woman says that he should have stuck with black. Or maybe a really dark gray.
In the game proper, there are numerous shout-outs: