In Star Wars: The Complete Saga and Indiana Jones: The Original Adventures, Harrison Ford's respective characters from each game appear as a Guest Fighter in the other.
The German pilot who fights Indiana Jones in Raiders of the Lost Ark is played by the same guy who plays the guy who operates the gong in Temple of Doom (the late Pat Roach). In the LEGO version, the German pilot is the guy who operates the gong.
In LEGO Indy 2, the title character is distracted while driving through the warehouse by the sight of you-know-who frozen in carbonite.
The "Shoot First" achievement for killing Greedo can be done with either Han or Indy.
Roger Craig Smith reprises his role of Captain America, but also voices Human Torch. Both are played by Chris Evans in their respectivefilms franchises. Pairing them together gets you the achievement of "Don't I Know You?"
Clancy Brown, well known for voicing Lex Luthor, reprises the role in LEGO Batman 2 and 3.
Laura Bailey as Black Widow. She had the same role in the Avengers Assemble! cartoon.
The majority of the voice actors in Batman 3 have had a history voicing those characters, like Gilbert Gottfried as Mxyzptlk or Tara Strong as Harley Quinn. Several voice actors from the Arkham games reprise their roles as some of the Bat-rogues.
Fandom Nod: In the "Raiders of the Lost Ark" hub in Lego Indiana Jones 2, we see a pig being roasted. It's not the official LEGO pig, but rather one made by BrickForge.
In most games, the roles aren't done by the original actors, but Clone Wars is an exception, being one of the first games to get the cast from the source (in this case, the show) to voice for the game, they even got James Earl Jones to do some voice clips for Darth Vader.
A good chunk of the voice cast changes for LEGO Batman 3.
Recycled Script: LEGO Marvel seems to take a lot from the first season of The Super Hero Squad Show: a cosmic object has broken and been scattered, so the heroes, based in the Helicarrier, must collect the pieces before Doctor Doom and his army of villains, all ending in Galactus attacking Earth and the two sides forming an Enemy Mine to stop him.
Trolling Creator: Due to fan demand for Raven for Beyond Gotham, the official Twitter account started teasing fans about it. Firstly, they jokingly asked if she was even that popular, then pretended to confuse her for Raven-Symoné by tweeting "#RevealRavenSymone". Finally they agreed to reveal Ra...'s Al Ghul.
Some files for the original LEGO Star Wars game shows that Zam Wessel was planned to be in the game, as well as a wheelbike chase with Grievous. They brought Zam back for The Complete Saga, but never used the wheelbike chase, presumably due to already having a driving segment.
Similarly, a level where you played as Anakin against the droid battleship in a Naboo Starfighter was planned for the first game (with a piece of the post-level cinematic shown in trailers) but was scrapped, most likely because Episode 1 already had the podracing level. It was included as a bonus level in The Complete Saga, redesigned to be more like that game's vehicle levels.
Demos for LEGO Marvel Superheroes showed that the Green Goblin could turn into his Ultimate incarnation. They are instead separate characters in the actual game.
Also, Lady Deathstrike was originally going to be in the game, but was cut.
The box art and the mini comic for stage five suggests that Tony was originally meant to upgrade to the Mk. 7. Instead he goes to Mk. 42
In one interview, the designers said they had considered giving Captain America a gun, but they decided it would be too difficult to add with his other abilities.
According to Brickipedia, the Lord of Apokolips himself, Darkseid, has character data that can be found by digging through the game files in LEGO Batman 2: DC Super Heroes. Nora Fries, the cryogenically frozen wife of Mr. Freeze, was also planned, but possibly scrapped due to lack of importance and canonically not making sense as a playable character.