In the credits of Lego Dimensions, the subtitles have a long ellipsis when GLADoS sings a long note, with commas inserted. If translated into binary code, with commas as 1's and periods as 0's, it reads as "1jhn1:9", or "1 John 1 v 9", a Bible verse corresponding to GLADoS' previous line "I forgive you everything":

In the opening cutscene of the Sonic the Hedgehog level pack, Dr. Eggman juggles six of the Chaos Emeralds in a similar fashion to the bad ending of the first Sonic the Hedgehog game.

In the opening cutscene of the Mission Impossible level pack, Jim Phelps watches an in-flight movie that features Ethan Hunt playing volleyball with a goose. This references the film "Top Gun", which also stars Ethan's actor Tom Cruise and features a scene in which he plays volleyball with a character named Goose.

In the final cutscene of the Portal level pack, Chell and Wheatley discover boxes with the logo of Black Mesa, the rival company to Aperture from the Half-Life game series.

In the chapter "Breaking the Barrier" of the Ghostbusters 2016 Story Pack, the parade float scene features balloons based on Ice King from Adventure Time, and Sonic and Dr. Eggman from Sonic the Hedgehog.

If Bane goes through a dimensional loading portal sequence, he mentions about this possibly being how Batman "got back into Gotham that one time". This references the 2012 film "The Dark Knight Rises", in which Batman was able to infamously return to Gotham City on lockdown, without any given explanation.

If Batman is placed with a duplicate of himself, he’ll ask if the other is some hockey pants wearing imposter from Gotham. This is a reference to the 2008 film The Dark Knight, in which Batman tells a Batman imposter that unlike him, he doesn’t wear hockey pants.

In the level "GLaD to See You" in the main story, HAL 9000 from the film "2001: A Space Odyssey" is summoned to distract GLaDOS. Unlike other cameos throughout the game, he’s the only character that's seemingly not made out of LEGO pieces.

If Sonic the Hedgehog and either Peter Venkman and Abby Yates are placed together, Sonic will ask them if they could take a look at a doll that looks like his best friend Tails. This is a reference to the Tails Doll that originated from Sonic R, another game developed by Traveller's Tales.

The Tails Doll also makes a cameo in the Marble Zone of the Sonic Level Pack.

If Sonic the Hedgehog is placed with a duplicate of himself, each will say "I found you, faker" and "I'll make you eat those words". This references Sonic’s interaction with Shadow on Prison Island in Sonic Adventure 2.

When Sonic the Hedgehog and Lumpy Space Princess are placed together, Sonic mentions about meeting a princess before getting uncomfortable and then saying he can’t remember. This references Sonic the Hedgehog 2006 and his questionable relationship with Princess Elise.

If Sonic the Hedgehog and Harley Quinn are placed together, Sonic will mention how he wants to keep his distance from Harley due to her red outfit and giant hammer. This references Amy Rose, who’s known for her red dress, giant hammer, and obsession towards Sonic.

If Sonic the Hedgehog is placed with Cyborg, he could ask if Dr. Eggman roboticized him (misspelled as roboticise). This is a reference to the concept of roboticization featured in media outside of the Sonic games, most notably the 1993 SatAM cartoon and Archie comics.

If Sonic the Hedgehog and Bart Simpson are together, Sonic may mention to Bart that if he sees a gold brick, he should “Just take it! Take it, take it, take it, take it! TAKE IT!”. This is a reference to The Simpsons episode “Marge Be Not Proud”, in which a vision of Sonic tells Bart the same thing about stealing a copy of the fictional game Bonestorm.

In test chambers 2, 6, 7, and 9 in the Portal add-on, it is possible to briefly spot Doug Rattman in various areas before he runs away.

In the Portal series, Doug Rattman is a scientist who worked for Aperture Science and is an integral part of the series lore. He is alluded to but never actually seen in the first two Portal games (though he did star in a promotional comic for Portal 2). This is technically the very first time players have physically seen Rattman in any official Portal game.

These Easter eggs were not discovered until over a year after the game had launched.

In the Doctor Who world, one of the comments the pedestrians will make is "I went to this GREAT pie shop. Used to be a barbers, y'know...", a reference to the Victorian penny dreadful character Sweeny Todd, the Demon Barber of Fleet Street.

If the console's internal clock is set to any fourth date of the month, i.e. 4th, 8th, 12th, etc. the TARDIS interior will feature the Fourth Doctor's alternate TARDIS interior.

In the opening cinematic, the number 42 splashes from the surface of Foundation Prime. The number 42 is a reference to The Hitchhiker's Guide to the Galaxy series where the number 42 is the "Answer to the Ultimate Question of Life, the Universe, and Everything".