Absent-Minded Professor: At one point, Indy tries to return to his office and is besieged by students because he hasn't been grading any of their work. He has to climb out the window to escape.
Ace Pilot: "Fly, yes. Land, no." Interestingly, in Temple of Doom, he says he doesn't know how to fly a plane. Guess he learned how to fly between then and Last Crusade.
It should be noted that Temple of Doom is a prequel to Raiders of the Lost Ark, the Last Crusade being a sequel to the latter.
Action Survivor: Indy may have styled himself as a badassaction hero, but in practice he's not much more than a slightly-greedy college professor who doesn't know when to quit.
Agent Scully: To a point. In Crystal Skull, Indy is a big skeptic about the existence of alien races, and in Raiders, considers the Ark of the Covenant nothing but a fancy gold box, but when the Ark is opened at the end of the film he insists that he and Marion avert their eyes.
Badass Normal: Unlike many superheroes he has no superpowers but has a large number of Improbable Aiming Skills (you know - the gun, the whip etc. etc.)
Berserk Button: One of the few ways to truly enrage the normally logical Henry Jones Junior is to harm an innocent child... just ask the shredded remains of Mola Ram in the bellies of a dozen satisfied crocodiles.
Disney Death: Similar to Basil from The Great Mouse Detective. In The Last Crusade Indy seems he's fallen to his death in a deep chasm along with Vogel. While his father, Brody, and Sallah peering over the cliff, believing that he died, Indy climbs onto the cliff edge, revealing he's jumped from the tank before it fell..
Disappeared Dad: Indy complained that his father was more concerned about artifacts in a museum than his own son. Notably, however, it was Indy that walked out on him.
The Gump: In the Young Indiana Jones Chronicles, if he or she has been written down in the history books in the last 100 years, Indy has met/befriended/fallen in love/fought/slept with him or her.
Honor Before Reason: In his younger days, as chronicled by the TV series. Becomes cold and jaded in adulthood, but regains this trope after reconciling with his father.
I Know Karate: Young Indiana Jones has shown proficiency in Northern Style Kung Fu in his TV series; though this is not retconned into the movie series proper, Indy has consistently been shown to be skilled in US Marines CQC (Close Quarters Combat, made famous by The Boss and Big Boss) since Temple of Doom; justifiable considering his extended experience in the military.
Jumped at the Call: He may be a world weary cynic but no one optionally does the kind of stuff Indy does without enjoying it just a bit.
Knight in Sour Armor: He is cynical most of the time, but has his romantic moments as well.
Line-of-Sight Name: "Henry Defense" came into being when he was asked to give a name while enlisting for the Belgium Army in World War I, and the French word "Defense' just happened to be on a plate resting on the desk.
Omniglot: Latin, Greek, Japanese, German, Mayan, Egyptian, French, Spanish, Arabic, Mandarin, Cantonese, Irish, Vietnamese, Hungarian, Hindi, Dutch, Old English, Quechua, and most likely others. Word Of God says he speaks 27 languages. Unfortunately, he didn't take that summer course in Hovitos...
This trope largely came about in the sequelfilms; in Raiders, scriptwriter Lawrence Kasdan intended Indy to be a rather poor hand with foreign languages (which is why he needs someone else to translate the Staff of Ra headpiece inscription).
Only Known by Their Nickname: All of his friends consistently refer to him as "Indiana" or "Indy". It wasn't until the third movie that people learned his first name is actually Henry, and that he got his nickname from their dog.
Sallah: What does it mean, this "junior"?
Henry: That's his name. Henry Jones, Junior.
Indy: I like Indiana.
Henry: We named the dog "Indiana"!
Sallah: You are named after a dog?!
Indy: I've got a lot of fond memories of that dog!
Papa Wolf: "They're innocent children... Mola Ram, prepare to meet Kali IN HELL!!"
And of course, to Mutt. When he thinks that Mutt is simply Marion's son, Indy looks out for him like anyone else with him on an adventure, but when he learns the truth, the trope is embodied full-on.
Badass Damsel: She knows pretty well how to use fire weapons and to fight. Moreover she must have a lot of nerves to face a sadist torturer like Toht and blowing smoke in his face.
Belligerent Sexual Tension - With Indy, of course. She punches him in the face when he first shows up in her bar.
Bottle Fairy: As demonstrated with Belloq, she could drink any man under the table.
Disney Death: In Raiders, Indy thinks she's dead when the truck she was thrown in while she was in a basket explodes. But he finds her alive at the Tanis site since they have switched baskets.
Badass Grandpa: Took down a German fighter plane with a fricking umbrella and a flock of seagulls... what a man!!
"I suddenly remembered my Charlemagne. 'Let my armies be the rocks and the trees and the birds in the sky.'"
Bus Crash: He's mentioned in the fourth film to have died sometime after the third. Justified since Sean Connery refused to come out of retirement just to make some cameo that would ultimately be insignificant.
Large Ham: When John Rhys-Davies is involved, there is no other path.
Took a Level in Dumbass: In Raiders, Sallah was competent, brave and intelligent. In Last Crusade, he was a borderline idiot savant comic relief character whose only redeeming characteristic was he could hit really hard.
YMMV on that. He knew that there was no museum in Iskendun, but the Nazis were too clever with the fake storefront leading to a truck. Is it because he wanted a few camels to compensate for his brother-in-law's car being blown up? That just makes him a good in-law! Also, do you realize how far it is to drive from Cairo in Egypt to Hatay in southern Turkey? Hundreds of miles. He was doing Indy a huge favor.
Professor Marcus Brody, Dean of Princeton University's Department of Archaeology.
Absent-Minded Professor: Smart enough to become the Dean of Archaeology at Princeton University, and yet can get lost inside his own museum, if Indy's word is to be believed.
The Cast Showoff: Mr. Elliot was an accomplished equestrian and so was able to safely nearly-fall-off-the-horse in the third movie.
Flanderization: From a slightly absent-minded professor who was implied to have Indy-like adventures himself to someone who needed to be handheld through every situation.
The Fool: Though he's not stupid, just a little bit of a clutz.
Aren't You Going to Ravish Me?: Willie during the entire scene where Indy bursts into her room to look for the secret entrance to Kali's temple. "I'm right here!"
Money, Dear Boy: Mild case with her actress Kate Capshaw, who although was a single mother feminist in Real Life, actually enjoyed playing a role that smeared all her ideals into the ground, calling it "the most fun I ever had in a role."
Well in that case it seemed like she was being a parody of every thing her views are against.
Meaningful Name: Apparently, her name is derived from the "Wilhelm Scream", which leads us to...
She's also named after Steven Spielberg's pet dog, much like how George Lucas had named Indy after his pet dog.
Generation Xerox: Acquires a visible facial scar through his weapon of choice, much like his father did on his chin with the whip. He even named himself Mutt.
Heroic Bastard: When he was born, his REAL parents were most certainly NOT married.
A God Am I: You'd almost think René got into this business just so he could hold idols over his head and make people bow to him.
Adventurer Archaeologist: The bad guy version of the trope. Plus, he's willing to let someone else do the adventuring while he waits outside to hold them up for the treasure at gunpoint.
Arch-Enemy: Well, the closest thing to it that Indy has.
In the Novelization, it's revealed that Belloq built his career around letting Jones do all the work, then swooping in to steal his artifacts/research papers.
Dragon-in-Chief: Nominally the main antagonist of the film, it's actually Nazi Colonel Dietrich who is the one in charge of the quest of the Ark and the one who calls all the shots. However Belloq uses his smooth talk and archeological expertise to sway Dietrich around to his point of view and get the colonel to do what he wants.
Even Evil Has Standards: Draws the line at rough treatment of women. René repeatedly tries to shield Marion from harm, though he's not overly enthusiastic about it.
Irony: If it weren't for the test he suggested that ultimately resulted in his and his co-villains Karmic Death on a remote island and delivered it to Berlin as is, there most likely would not have been a World War II because of the Ark blowing it up.
Loveable Rogue: Tries to present himself as this to Marion, and succeeds at first. This illusion is probably shattered for good later when a captured Marion gets shoved around by a soldier and Belloq coldly brushes by without a word.
Manipulative Bastard: Gets into the heads of and manipulates the natives of South America, Marion, and even Indy himself.
Even Evil Has Standards: Does a very minor one when he seizes the smuggling ship. Captain Katanga tries to protect Marion by implying that he plans to sell her as a Sex Slave, hoping that after the Nazis get their cargo back and find no trace of Indy they'll be satisfied. Instead a visibly disgusted Dietrich immediately grabs Marion and threatens to sink Katanga's ship.
Satellite Character: Major Gobler, his ever-present second in command. Even the novelization emphasizes Gobler as "Dietrich's shadow" and little else.
The Stoic: Indiana Jones hijacking the truck carrying the Ark and all the wild driving his Mercedes is put through as a result? It barely earns a raised eyebrow and a mild frown from him.
Not So Stoic: Although Indy continually coming out of nowhere to ruin his mission eventually starts getting to him, both with the tossing a melon at a dog thing and when his men can't find Indy on the smuggler's ship. "WHAT ABOUT JONES?!!"
Wicked Cultured: Listens to a record player and drinks bourbon from a cut crystal decanter outside his tent in Tanis.
Dyeing for Your Art: Ronald Lacey was not actually balding. In films before and after Raiders of the Lost Ark, he has a full head of hair. However he shaved the top portion of his head but left the hair on the sides and back to give Toht male pattern baldness.
Fake Nationality: Ronald Lacey is English playing a German villain.
We Have Reserves: At one point he instructs a mook to shoot both Indy and another mook who are in the middle of wrestling for possession of a gun. Backfires spectacularly, since now Indy and said mook both want to shoot the same guy with the gun.
Badass Boast: "The British in India will be slaughtered. Then we will overrun the Muslims. Then the Hebrew God will fall. And then the Christian God will be cast down and forgotten. Soon, Kali-ma will RULE THE WORLD!!"
Bald of Evil: He wears an animal skull for his rituals, but has not a hair on his head save for his eyebrows.
Beat Still, My Heart: See the page picture. Possibly the most famous example of this trope.
Brainwashed and Crazy: The shooting script and novelization had Mola Ram have the same confused and bewildered, snapping-out-of-brainwashing reaction as everyone else that was mind-controlled after handling the glowing stone. In those version he looks confused and terrified for a second, then falls to the crocodiles. The final film, however, does not have this, leaving him solely as a Complete Monster.
Uh, no no no, if you had been paying attention, he was probably doing that to try and see if the stones had any actual power, which were created by Shiva, which had been hinted at by a mural to be how to uses them.
It might not much a stretch. From Hindu mythology, Shiva IS a supreme god and one of Hindu Trinity. He is also a god of destruction and Kali husband. So Indy might have a point here. (Although I need some expert to confirm this).
Dyeing for Your Art: Amrish Puri shaved his hair for this film, and because of his iconic performance, he kept his bald appearance for the rest of his life.
Faux Affably Evil: When Indy is captured by the cultists, Mola Ram is quite lighthearted, with big, creepy smiles and a mellow voice... his laugh is quite off-putting, as well.
Large Ham: "Drop them, DOCTOR JONES! The stones will be found... YOU WON'T!"
Mean Character, Nice Actor: Amrish Puri, a professional wrestler, is said by Harrison Ford to be one of the sweetest and kindest men he has ever worked with.
Not In This For Your Revolution: Hinted at a few times, yet ultimately subverted; Elsa detests the Nazis for destroying art, but her greed trumps any righteous indignation.
Take That Kiss: "This is how we say goodbye in Austria."
Combat Pragmatist: Following on from below, Vogel has no problem using chains and shovels to beat up the good doctor. He also enjoys punching Indy in the face when our hero is strapped into a chair.
Disney Villain Death: Averted. We see Vogel's body get thrown around like a ragdoll and crushed when his tank plummets over the side of a cliff.
Deadpan Snarker: "This is how we say goodbye... in Germany." *Face punch*
Dragon-in-Chief: Donovan may have had the money and knowledge, but it is Vogel who controlled the military might of the Nazi Grail-expedition.
Fail O'Suckyname: The German word Vogel, which means "bird," is often used as "idiot." Unfortunately for the colonel, the word ernst also means "seriously." Der Oberst Ernst Vogel ist ernst ein Vogel!
Affably Evil: Out of all of Indy's foes, she treats him with the most respect and as an equal. She also showed genuine horror and sadness at the death of Dovchenko, implying that she saw the fellow colonel as a friend rather than just a tool.
I Know Karate: According to Cate Blanchett, Irina knows Shotokan-Ryu Karate to be exact. However, considering Irina's vocation as a Russian soldier, its more likely to be the Soviet Military art of Sambo.
Tragic Villain: Her lust for knowledge lead to her destruction.
George "Mac" McHale
Death Equals Redemption: For what it's worth, he regarded Indy as a friend to the very end, and let himself be dragged into oblivion so Indy wouldn't be dragged down with him.
I Know Karate: Specifically, the Russian Military martial art of Sambo, which focuses on throws, grappling and painful joint-locks/breaks. Combined with his already impressive size and strength, Dovchenko's mastery of Sambo almost allowed him to kill Indy were it not for the timely presence of a tree branch...
Mighty Glacier: Though relying more on technique and skill rather than brute force alone.