If I'm missing anybody lemme know! This is including everyone.
If several guys died at once I list them together.
Peru, the Opening Sequence:
Satipo - Impaled on spike trap.
Barranca - Shot with poison darts by the Hovitos.
Nepal, the Bar Fight:
Ratty Nepalese - Set on fire; shot in the face by Indy. (Definite kill for Indy.)
Second Nazi - Shot by Indy and the Giant Sherpa. (Definite kill for Indy.)
Giant Sherpa - Knocked unconscious by Indy; dies in burning Raven. (Indirect kill for Indy.)
Mean Mongolian - Shot in the back by Marion.
Streets of Cairo
Cairo Henchman - Accidentally stabbed by one of his buddies.
Cairo Swordsman - Shot by Indy. (Definite kill for Indy.)
Cairo Henchman on Truck #1 - Shot by Indy; falls off truck. (Definite kill for Indy.)
Cairo Henchman on Truck #2 - Shot by Indy; blown up in exploding truck. (Definite kill for Indy.)
Gestapo Agent - Blown up in exploding truck. (Definite kill for Indy.)
Tanis Airfield
Truckload of German Soldiers - Shot by Marion.
German Mechanic - Chopped by Flying Wing prop. (Indirect kill for Indy.)
German Pilot - Knocked unconscious by Marion; blown up in exploding Flying Wing.
Road to Cairo
Major Gobler, Lieutenant Belzig and German Soldier - Fly off cliff in troop car. (Definite kill for Indy.)
Tough Sergeant - Thrown out the truck windshield by Indy and run over. (Definite kill for Indy.)
Nazi Island, the Tabernacle
A Whole Lot of German Soldiers - Shot with lightning from the Ark, burned up in Holy Fire.
Colonel Herman Dietrich - Head implodes from the power of the Ark, body consumed by Holy Fire.
Major Arnold Toht - Head melts from the power of the Ark; body consumed by Holy Fire.
Rene Belloq - Consumed by Holy Fire, his head explodes.
Shanghai, Club Obi-Wan
Wu Han - Shot by Chen.
Chen - Impaled with a flaming shish-kebab by Indy. (Definite kill for Indy.)
Streets of Shanghai
Henchman - Shot in the face by Indy. (Definite kill for Indy.)
Pankot Palace
Thuggee Assassin - Tangled in Indy's whip, pulled into the ceiling fan and hung. (Possibly indirect kill for Indy.)
Temple of Doom:
Sacrifice Victim - Heart ripped out by Mola Ram; lowered into lava by Thuggee priests.
Thuggee Guard - Hangs onto Ladder as it drops from a great height.
Thuggee Priest #1 - Pole-vaulted into lava by Indy. (Definite kill for Indy.)
Thuggee Priest #2 - Pole-vaulted into lava by Indy. (Definite kill for Indy.)
Chief Guard - Pulled into rock crusher and ground up. (Indirect kill for Indy.)
Mine Cart Chase:
3 Thuggee Guards - Crash in mine cart; rammed into by second mine cart of guards.
Thuggee Guard in Mine - Run over by second mine cart. (Definite kill for Indy; Indy threw him onto the tracks.)
2 Thuggee Guards - Hit guard on the tracks and go flying down a chasm. (Indirect kill for Indy; they wouldn't have hit the other guard if Indy hadn't thrown him on the tracks.)
Bridge at the End
A Whole Lot of Thuggee Guards - Fall and get eaten by alligators when Indy cuts the bridge. (Definite kill for Indy.)
3 Thuggee Guards - Lose their grip and fall and get eaten by alligators. (Indirect kill for Indy; they lose their grips when the bridge hits the cliff.)
Thuggee Guard on Bridge #1 - Falls and gets eaten by alligators.
Thuggee Guard on Bridge #2 - Knocked loose by Mola Ram; falls and gets eaten by alligators.
Mola Ram - Burns his hand on Sankara Stone, falls and gets eaten by alligators. (Possibly definite kill for Indy.)
Some More Thuggee Guards - Shot by British soldiers.
Portugese Coast, the S.S. Coronado:
Henchman - Knocked off the Coronado by Indy. (Definite kill for Indy.)
Panama Hat and Several Henchman - Blown up with the Coronado.
Venice, the Boat Chase:
3 Cruciform Sword Members - Crushed between two ships and blow up.
Castle Brunwald and Escape:
2 German Soldiers - Machine-gunned by Indy. (Definite kill for Indy.)
Several Nazi Officers - Trapped in burning dining room when Indy jams the door with a bust of Hitler. (Definite kill for Indy.)
German Soldier on Motorcycle - Goes flying when Indy jams a flagpole into his wheel spokes. (Definite kill for Indy.)
Escaping from Germany:
German Pilot #1 - Tries to fly into a tunnel, loses his wings, zooms past Indy and Henry and blows up.
German Pilot #2 - Blinded by seagulls, crashes into a cliff.
Hatay, Canyon of the Crescent Moon:
Several Cruciform Sword Members - Shot by German soldiers.
Kazim - Shot by German soldiers.
German Soldier in Kubelwagon - Gets stuck on tank barrel, then shot off and run over. (Possibly indirect kill for Indy; since even though Vogel gave the order to fire it's Indy's fault the Kubelwagon got stuck on the tank.)
Hatayan Tank Gunner - Killed when the gun jams and blows up in his face. (Definite kill for Indy.)
3 German Soldiers on Tank - Shot by Indy; the bullet goes through all three of them. (Definite kill for Indy.)
German Soldier on Tank - Knocked onto the treads, rolls off and is crushed. (Definite kill for Indy.)
Truckload of German Soldiers - Blown up with the tank's other gun by Henry.
German Soldier in Tank #1 - Knocked unconscious by spinning periscope; goes over cliff in tank. (Indirect kill for Indy; he's the one who kicked the periscope.)
German Soldier in Tank #2 - Bonked by Marcus with a shell; goes over cliff in tank.
Hatayan Tank Driver - Catches a stray bullet in the forehead.
Colonel Ernst Vogel - Rides the tank all the way down the canyon.
(Marcus is actually Vogel's indirect killer because by hitting the soldier with the shell he indirectly caused the tank driver's death, thus causing the unguided tank to go over the cliff in the first place.)
Temple of the Sun:
Hatayan Soldier #1 - Decapitated by the Breath of God.
Hatayan Soldier #2 - Decapitated by the Breath of God.
Walter Donovan - Drinks from the wrong Grail; ages into dust.
Dr. Elsa Schneider - Falls down a big crack in the floor.
Nevada, Area 51 and Doom Town:
MP Sergeant and 3 MPs - Shot by disguised Soviet soldiers.
A Whole Lot of Soviet Soldiers - Fried by backwash from the rocket sled. (Indirect kill for Indy; the sled fired up because he knocked Dovchenko into the control panel.)
3 Soviet Soldiers - Incinerated by nuclear blast.
Chauchilla Cemetery:
Cemetery Guard: Shot with his own poison dart by Indy. (Definite kill for Indy.)
The Road to Akator, Jungle Chase:
Soviet Soldier in Jungle Cutter - Blown up when Indy shoots the Cutter with a rocket launcher. (Definite kill for Indy.)
Soviet Soldier - Eaten by giant ants.
Colonel Antonin Dovchenko - Eaten by giant ants. (Possibly indirect kill for Indy; he knocked him into the ants.)
Several Soviet Soldiers - Fall off cliff when smacked with tree branch.
Akator:
All (?) of the Ugha Tribesmen - Massacred by the Soviets.
4 Soviet Soldiers - Sucked into dimensional vortex.
Irina Spalko - Eyes burned out and head explodes from Too Much Knowedge; presumably sucked into dimensional vortex.
George "Mac" McHale - Sucked into dimensional vortex.
(I don't believe the Grail Knight is supposed to haved died, merely been trapped in the temple by the collapsing entrance.)