Marco Bott. Even though the series has a high body count, and many trainees die during the Battle of Trost, he is the only member of the Top 10 killed in action. This leaves his comrades deeply shaken, as he provided vital leadership and emotional support to the others. In particular, it inspires Jean's evolution from a selfish and cynical jerk into a capable young leader — abandoning his dreams of an easy life with the Military Police Brigade in favor of joining the Survey Corps. There's also the very sinister hints about the circumstances surrounding his death, when his missing gear turns up...
The majority of the veteran officers in the Survey Corps, in particular the members of the Special Operations Squad. Their deaths at the hand of the Female Titan drives home just how dangerous she is compared to normal Titans.
Willy Tybur's character is a Mr. Exposition who gives a speech about how evil Eren Yeager is, declares war on the Eldians that live on Paradis Island, and is then promptly killed by Eren in his Titan form. This seems to have been somewhat of a Batman Gambit however, as Willy was prepared to die in order to lure out the enemy that he knew was hiding amongst them.
In Berserk, every member of the Band of the Hawk who isn't Guts, Griffith or Casca dies horribly at the end of the Golden Age Arc after Griffith makes his Deal with the Devil and marks everyone for sacrifice to the Godhand. Guts barely survives, losing an eye and an arm, and Casca is left traumatized to the point of insanity. The only other survivor of it all was Rickert, who had the good fortune to not be with the general group when the Eclipse went down.
Bleach: In spite of his minor role, Choujiro Sasakibe's death is not only violent and bloody, but plays out as a major Wham Episode, due to no good guy dying before this. It also seemed to have a lasting impact on Yamamoto and Byakuya's attitudes towards the Vandenreich. Yamamoto became much more angry, aggressive and impulsive than normal and Byakuya became more merciless.
In Blood+, George asks to be killed by Saya before Delta 67 could turn him into a monster.
Hideyuki Makimura, Ryo's partner and best friend is murdered by Union Teope.
Mick Angel too: his death at the hands of Union Teope serves to show that shit has hit the fan hard.
Teresa of the Faint Smile in Claymore. More a variant of this trope, as we know she's dead from the start, but are shown her story (and thus Clare's backstory) about a third of the way through the main plot, and if the backstory were presented first, the audience would never see it coming.
It then happens again later on to show just how out of their league the Claymores are in the Northern campaign, where Rigald takes out Undine, Veronica, Jean, and Flora in rapid succession. Although Veronica was basically a Mauve Shirt, the other three had all gotten fair amounts of character development by this point, and only Jean was able to hang onto life long enough to make her death shift from "shocking" to "tragic."
Leomon in the Digimon Franchise. Incidentally, he's an actual lion. This is a recurring in-joke for the meta-series which the directors are entirely aware of. When they were deciding on which digimon would be killed during Digimon Tamers they chose Leomon simply because he had been killed before. Other seasons seem to follow suit and at least one Leomon is killed per continuity.
This trope has become so prominent that the writer of Tamers had to apologize on Twitter for starting this trend. He added that if he ever wrote another Digimon story, he'd have Leomon survive to break the tradition.
Bora's death at the hands of Mercenary Tao. His first appearance had him being strong enough to take out an entire unit of the Red Ribbon Army long before Goku got there, and was also a noble Indian. He ends up impaled by his own spear by Tao and the goal of the remaining arc is gathering all of the Dragon Balls to bring him Back from the Dead.
Following this, Krillin is killed at the conclusion of the 22nd Tournament arc by the minion of a villain we haven't met yet, providing the first death of a major character in the series that emphasizes just how awful the new villain, the great Demon King Piccolo, truly is. This is further emphasized by the deaths of Master Roshi and Chaiotzu later in the same arc.
In Dragon Ball Z we have three Sacrificial Lions. The first is Dende, who is killed near-instantly by Frieza once he reaches his final form. Later in the battle is the death of Krillin (which is what pushes Goku over the edge to attain Super Saiyan). Much later in the next arc is Future Trunks, to show just how bad things in the Cell Saga have gotten. All of them get better, though the Namekian Dragon Balls are needed in Krillin's case due to this being the second time he was killed, since the Dragon Balls of Earth can't be used to grant the same wish twice.
Movie example. Lieutenant Blue, the movie's (arguably) Good Counterpart of General Blue in Mystical Adventure was this. He tried to warn Emperor Chiaotzu about Tao and Shen's treacherous ambitions after somehow stumbling on Ran Ran, Chiaotzu's wife, in Shen's bedroom, which got him killed by Tao.
Rei, one of the leading heroes of the series, dies pretty late on in the series after he tries to take on Raoh, who is just as badass as Kenshiro and has the same deadly style of Hokuto Shinken. With the help of a technique from Toki, he survives just long enough to take down his rival Yuda and make it so that the Star of Death does not appear for Mamiya, the woman he loves, anymore. Rei's death marks a turning point for the saga.
The Souther arc has Shuu, one of the most kindhearted badasses of the entire saga, who dies in supremely heinous fashion by Souther, the main villain of the arc and one of the most despicable villains yet. He dies after being forced to make his way up an enormous pyramid with cut tendons, holding the enormous stone cap piece meant to finish it, with Souther ordering his men to kill every slave present if he drops it, and to execute the families of anyone who helps him. Once Shu finally does make it to the top of that pyramid Souther orders his archers to put arrows into Shu before finishing him off with a thrown spear. This act cements Souther as one of the most horrible villains of the series, and Kenshiro is appropriately infuriated, setting the stage for an epic showdown.
The lovable Maes Hughes of Fullmetal Alchemist dies a ways into both versions of the series (but especially in the 2003 anime, where his death was one of the cruelest twists in the series). He was already well underway to unraveling the plot before the main protagonists (and it's not until a good deal later that the protagonists and the audience discover just how close Hughes had come to figuring out the villains' scheme) and even manages to get the drop on his assassin. Unfortunately, the assassin wasn't human.
Ryu Jose from Mobile Suit Gundam went out in a Heroic Sacrifice just under halfway through the series. His death ended up making everyone on the White Base stronger. Perhaps as an intentional mirror of the audience, Amuro initially refused to believe that Ryu was really dead after Sayla tried to break the news to him.
Gavane Gooney in ∀ Gundam. Hebecomes an important secondary character when Lousana joins as a faction in the Earth-Moonrace conflict, a bold Ace Pilot whose squad of excavated Zakus take a prominent role in the battles with Dianna Counter. He also strikes up a romance with Sochie and asks to marry her. When he dies in the "midnight sunrise" of the ancient nuclear warheads, the conflict suddenly changes from a scrap over territory rights into an existential threat to humanity itself... as well as foreshadowing of the Dark History that threw Earth back from the space age to their present level of technology.
Even something like If Only It's An Ideal Daughter, Would You Even Pamper the World's Strongest? has an example. Selika (also transliterated as Selka, Serika, Celica, and Cerica) is quickly introduced as The Rival, being an S Rank like Yukina, and whose sole sense of worth comes from being a prodigy on the front lines to save humanity. Just after she gets a ton of Character Development, terrorists attack unexpectedly while the girls are at the mall, and Yukina and Selika transform and fight them, only for Selika to get hit, and transformed into a Venom's Derm herself, meaning she must be put down. Then her only living relative cries over her body and Yukina decides to join the monster-fighting group she had previously turned down, because Selika's death proved that no one is safe, not even in the underground mega-cities that are humanity's last redoubt.
The 'Stardust Crusaders' arc in particular has plenty of characters to dispose of to show how dangerous Jotaro's opponents are.
And 'Stone Ocean', which is more explicit that the main characters drop like flies due to how powerful the Big Bad becomes. Even Jotaro himself and the arc's protagonist Jolyne die. In fact, all the fighters die sacrificing themselves while the Non-ActionKid Hero survives and saves the day.
The whole Zeppeli family has this as their role in the other arcs. They show up stronger than Jojo on their first appearances, teach or train alongside him until they're closely matched, then die against a superior opponent, leaving him the power to avenge them.
Legend of Galactic Heroes has two separate instances of this trope. The first is Kircheis, Reinhard's best friend and equal, who takes a bullet for him a quarter of the way through. The second is Yang Wenli, the main character next to Reinhard, who is shot in the leg and dies from blood loss three-quarters of the way through.
Mazinger Z's Professor Morimori was a major part of the heroes' team up until Episode 79, where he lured some of the Iron Cross Corps into their own minefield trap and died in the process. His loss was mourned by his companions and the rest of the staff.
Richard Braun from Monster, Driven to Suicide after several chapters/episodes where he appeared to be the main character of the Munich arc.
HiruzenSarutobi, the Third Hokage , who went out fighting Orochimaru, the Big Bad of Part 1. Even though he goes via Heroic Sacrifice, it still counts as the villain had pushed him into a spot with no alternative, and was the first major "good guy" death (2nd following Hayate Gekko). It also has a huge impact and lasting consequences (specifically, being replaced in his station by Tsunade). His son Asuma, Team Leader for Team 10 qualifies even moreso, dying partway into Part 2 and embellishing how dangerous Akatsuki members are. Incidentally, in the two anime adaptations both Sarutobi men die in Episode 80.
Ao, Shikaku Nara, Inoichi Yamanaka, and the rest of the sensors have been killed after the alliance's HQ was attacked by the Juubi, just to show how dangerous the damn thing is. Made extra poignant by Shikaku's determination to stay there and make sure he gets one final message out to the alliance, despite knowing full well that none of them will make it out alive.
Of course, by the end of End of Evangelion, HUMANITY disappeared off the face of the earth by being tangified, so note depending on whether you think he took Shinji's offer to reconstitute himself back into an individual being it's pretty clear where he ended up.
One Piece: Whitebeard, whose death had a huge impact on the whole world, and Ace, whose death had a huge impact on Luffy.
Gesicht, the main character of Pluto, is murdered three-quarters of the way through. The other robots would count as well.
Shusei in Psycho-Pass in Episode 16. The plot seems as if it will suddenly wrap up in this episode, despite more episodes left in the season...and then it is revealed that Choe has managed to see the Sibyl System, something that arguably controls the majority of society. Shusei follows him into the room where the Sibyl System is located...and then Choe gets shot by the Police Chief who shows up almost out of nowhere, with a Dominator that makes his head asplode. Shusei is relaxed, since he is technically a cop and Choe was an accomplice to Makishima who had been caught earlier in the plot. Turns out, the chief wants Shusei dead as well and Shusei finds out the chief is a Cyborg...right before he is also shot with the Dominator, in a way that guarantees a messy death.
Kamina . He started off as a Decoy Protagonist, and his death one third of the way through the show sends the main character into a Heroic BSoD.
Kittan as well, along with all the minor pilots.
The Movie of the series changes this so the minor pilots live to the end and assist in the final battle.
Ginshi Shirazu in Tokyo Ghoul :Re. In the lead-up to the operation, Shirazu becomes a focal character as he struggles with his responsibilities as Squad Leader, caring for his hospitalized little sister, and coming to grips with using the weapon made from his first major kill. During the operation, the team encounters Noro and quickly finds themselves overwhelmed by the seemingly-invincible Ghoul. Shirazu overcomes his fear of using his Quinque, landing a devastating blow and seemingly bringing down the horror. But Noro revives for a surprise attack, leaving Shirazu alone and fighting with everything he has to defend his injured comrades. Shirazu pushes his Power Limiter to the breaking point, and manages to land devastating attacks that create an opening for Urie to finish the creature off......but ends up ripped almost completely in half in the process. He ends up slowly bleeding to death in Urie's arms, and his body is later stolen by Aogiri Tree in order to steal the Quinx Surgery. The Quinx Squad ends up broken up, with Mutsuki reassigned to other squads and their mentor, Sasaki, resigning and abandoning them.
Starscream meets his end this way in Transformers Armada. After battling with Megatron and trying to convince him that Unicron is the real threat, he finally attacks Unicron himself and is destroyed in one shot. (Of course, considering how much damage he'd taken already, it was hardly a surprise.)
Aina Sakurai of Valvrave the Liberator. She's a close friend to the main cast, and is one of the few people who knows the secret curse of the Valvrave pilots. Then, she is killed, unsurprisingly for a small girl caught in the middle of a 0-gravity combat zone. Her death serves to focus the minds of all the people in the school, serving as a reminder that things are serious now, and giving a few characters someone to avenge.
In Yu-Gi-Oh! GX, there were lots of them. Both Jim and O'Brien became this, fighting Dark Duels against the Supreme King in an attempt to save Judai (with O'Brien knowing he'd likely be killed). Edo Phoenix became one later trying to save Echo from Amon, and Kaiser did so in an attempt to fight Yubel (knowing he was dying but hoping to take her with him). In all cases, fortunately, they were Not Quite Dead and were restored later.
Jun Manjoume is basically this trope, often non-lethally. In the first season, he is one of the two Key Guardians who are defeated off-screen by Amnael. In the second season, he is the first student to be brainwashed by Saiou. In the third season, he's the first major character turned into a "Duel Zombie" and is later the first sacrifice for the card Super Polymerization.