Accidental Pervert: Or is it? When Indy and Sophia enter completely dark rooms the "Look" command is replaced with "Touch". Indy can "touch" Sophia, to which she'll respond with a smart remark (e.g. "Hands off, Jones!", "Is that a ship rib in your pocket, Or Are You Just Happy to See Me?") or even an audible slap to Indy's face
Actor Allusion: Well, to the original portrayer, anyway: in Indy's office is a collection of letters to Indy's school from Henry Jones Sr. that all begin the same way — "Regarding Henry", a Ford film from the '90s.
All There in the Manual: The comic adaptation explains a lot, like the connection between the Atlanteans' Schizo Tech and the reason for the God Machine. It was aliens. They had horns, gave the Atlanteans some technology and Orichalcum, and when they left, the Atlanteans, misguided souls that they were, tried to bring them back by turning normal people into "gods." Unfortunately, it didn't work and they became mutants.
As Long as It Sounds Foreign: The controls for the Nazi submarine are labeled "Ausgeschnitzel", "Flugeldufel" and "Krauskefarben". (Clearly the games had substantially less budget for translators than the films.)
Fridge Brilliance: Indy doesn't speak German, so even if the player does, the labels still don't help...
Bittersweet Ending: The bad ending - the Nazis are defeated and Atlantis is destroyed, but at the cost of Sophia's life.
Body Horror: The innermost sections of Atlantis are littered with the twisted skeletons of people mutated by the Atlanteans' failed experiments with their ascension machine. When Klaus Kerner decides to try the machine himself, he ends up transforming first into a giant, then into a stunted minotaur.
Convection Schmonvection: Indy and Sophia have to cross a lava flow at one point, using stepping stones that were previously buried in the lava flow- and will be again if you waste too much time getting across.
Dummied Out: The game code features several rooms which are never even seen in the finished game, including an entire section based around Sophia's apartment (which was relegated to only being an unplayable Cut Scene in the final version).
Have a Nice Death / It's a Wonderful Failure: Game Over screens will usually be accompanied by a text explaining Dr. Jones' death and/or what happened after. An example: "Indy's failure to subdue a sixty-year-old U-boat captain allowed the Nazis to conquer the world."
Historical In-Joke: Indy wonders why the Minoan civilization had this obsession with bull-headed figures (like the tale of the Minotaur living in a labyrinth underneath Knossos); it's implied that the Minoans tried to imitate the style of Atlantis and it's very likely that they got their hands on a few of the Atlantean horned mutants product of their failed experiments (maybe the King Minos' Minotaur was one).
I Love Nuclear Power: The Nazis, The Atlanteans. The good guys are afraid they want orichalcum for nefarious purposes, since a single bead contains enormous power. It turns out They want to use it to turn on the god machine.
Imported Alien Phlebotinum: Atlantean artifacts all around the globe. Orichalcum averts this oddly enough, since it does actually originate from Earth, but is exceptionally rare and requires some advanced technology to mine and process.
It Will Never Catch On: In the comic book adaptation, Indy says that he considers continental drift a nutty idea (although still more plausible than the existence of Atlantis)— an opinion a lot of 1930s scientists would have shared. Of course, later in the story, he ends up in... well, look at the title.
Jerk Ass: Many of the characters you encounter, but especially Dr. Heimdall.
Last Lousy Point: The game's "Indy Quotient" score keeps track of points found in each of the three paths players can take, so you have to play all three routes (multiple times each) to get a perfect score. And some of the points involve fighting the biggest, toughest guys in the game instead of getting around them through puzzle-solving.
Monologuing: When Sophia!Nur-ab-sal enters the throne room.
Multiple Endings: Depending on whether or not you rescue Sophia and convince Ubermann to test the machine on himself.
Mundane Utility: Lead is impervious to orichalcum, and amber can be used to dowse for it.
No OSHA Compliance: Some of the archaeological digs Indy is forced to explore, not to mention Atlantis itself.
Offscreen Inertia: Played with. When you meet the Norwegian archaeologist, he constantly digs in the same spot (as is common of adventure games of this era). When you leave and come back, he has frozen to death, apparently never having left the cave.
Painting the Medium: In a manner of speaking. One puzzle involves Indy turning on a generator in a darkened underground dig site. If the player waits, Indy's eyes will adjust and you'll be able to see what you are doing.
Save Scumming: The only post-Monkey IslandLucasArts adventure game where this is necessary. You generally don't have to worry about it on the "Teamwork" and "Wits" paths unless you're thinking of doing something really stupid, but it's practically a requirement for getting through the "Fists" path.
Scenic Tour Level: The opening sequence has Indy appear to be breaking into a secret stash of artifacts... only for it to be gradually revealed that he's in Barnett College and only swung through the window because the door was blocked. He then falls through multiple floors slapstick-style.
Schizo Tech: Justified since orichalcum is a clean, safe source of nuclear power of some sort.
Shown Their Work: The developers clearly went on researching everything about the myth of Atlantis, designing the architectural style of Atlantis as if the Real Life Minoan was inspired by it. The manual cites all the books and sources the developers consulted.
Slap-Slap-Kiss: Indy and Sophia after rescuing Sophia from the dungeon.
Smug Snake: Kerner and Ubermann, who are convinced that the very same machine that horribly mutated scores of Atlanteans will work on them because of their superior Aryan qualities. They find out the hard way that they are wrong.
Soul Jar: Sophia Hapgood channels the spirit of the last Atlantean King through her necklace. It's a reliquary for Nur-ab-sal, and Indy has to take it from her by powering it up with orichalcum, whereupon it morphs into a demonic face.
Story Branching: Early on the player must choose one of three paths: The "Team" path has Sophia Hapgood join Indy as backup, the "Wits" path has a plethora of complex puzzles, and the "Fists" path has lots of action sequences and fist-fighting. Each path has a different plot, including different cutscenes and locations to visit. Some needed items in a given path become useless in another one. Story and gameplay converge again in Atlantis, with some room for Multiple Endings as mentioned above.
And also the car chase in Monte Carlo. It is an Indy game though.
Don't forget the fist fights, although these are thankfully skippable if you hold the right button (number-pad 0, the "sucker punch") during the fight. You don't get the points for your Indy Quotient if you do this though. Plus, the only character on which the sucker punch DOESN'T work has a health bar that reaches off the screen, and he just laughs at you and socks you in half if you try it. If you take Indy on the "Fists" gameplay path, he's in the labyrinth at Crete, at the bottom of a long natural ramp. At the top is a boulder that needs to be dislodged. You know what to do.
Unobtanium: The adventure begins when the Nazis steal a bead of orichalcum from Indy; it's portrayed as an incredibly powerful energy source (and a set of Interchangeable Antimatter Keys for many of the game's puzzles), and most of the game is a race for the motherlode at Atlantis itself.
Unwinnable: You can break the doors to the middle ring by trying to open them without boiling away the water. Possibly due to an oversight of Lucasarts' policy.
Walk into Mordor: While Atlantis is inaccessible for justified reasons, to get to the Third Circle of Atlantis you have to use an orichalcum-powered Bronze Age tunnel-boring machine, which promptly falls into the lava.