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.
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.
The Other Wiki states that for LEGO Batman 3, Aquaman will be voiced by Scott Porter, instead of Brian Bloom. Additionally, Josh Keaton takes over as Green Lantern from Cam Clarke, while Mark Rolston (Lex Luthor) and Richard Epcar (Joker) take over from Clancy Brown and Christopher Corey Smith.
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.
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