Alternate Destination: Gaia gave up on her position of a powerful, immortal spirit to resurrect the dead protagonist, which ended up killing her in the long run. At the end of the story, when it seems everything has been undone, we learn that she's NOT coming back.
In chapter 10 Gendo got shot by a SEELE member and died in Shinji's arms.
All SEELE members in the last chapter, turned into LCL by Rei.
Clash of the Elements: In Part 1, All the Outer Guardians Minus Driad, the Genesis Samurais (Physically anyways, and Joe Dark
In Movie 1, Tabuu
In Part 2, All of Smithy's creations minus Axem Red, Smithy himself, Dimentio, Cackletta, Chaos Alex, and Alex Whiter
In the What-Ifs, Not counting the millions of people that are erased in the cataclysmic events that unfold we got Alex Whiter and Joe Dark/Dark King in Demise Under the Stars and Alex Whiter, Tabuu and Cackletta in Return to a Blank Slate
In Despair's Last Resort, Kaito, Naomi, Shigeru, Shizuka, Miyako, and Saemi are confirmed to be dead forever due to the damage caused during their deaths in the simulation.
In Perfection Is Overrated, the death toll includes all of the SUEs, Kyoko, Ishigami, Yukariko, Miyu, Nagi, The Usurper and The Obsidian Lord. Unlike in canon, anyone who dies here stays dead, as a result of Miyu's destruction late in the fic.
In the main timeline, Shining Armor's friends Sunset and Private Ranger are all killed in action while stopping a mega storm.
In the Dark World Arc, it being a thousand years later, nearly everyone who wasn't immortal (or made immortal by Discord) is long dead. However, at the end Rarity's newly ascended Alicorn self, Queen Libra, is allowed to resurrect everyone who was killed by Discord or his forces, but due to the rules, some DO stay dead. Big Mac died of old age and Pinkie Pie and Fluttershy both died well after their natural life span, for example, so they do stay dead. Cadence was also killed in a Last Stand and didn't return, but she's a goddess so she is simply helping from the afterlife. Queen Chrysalis was also absorbed by Cadence and is likewise dead for good.
The Bully: Iona MacEachern and her boyfriend Craig Sullivan were drowned by their swimming teacher in "Harry Smith's Swimming Lesson", Steven McMullen received a "poisonous government injection" in "Harry Smith's Poisonous Government Injection" and four characters were killed by Euan Milton in "The Destruction of Colham High School".
From Young Justice: Darkness Falls: We have Vandal Savage, Glorious Godfrey, Volcanna, Doomsday, Klarion. A pretty high body count considering the canon show was a bit more conservative with its deaths. In additions, several heroes are either Not Quite Dead or come Back from the Dead, meaning there's less of a net loss than this list might indicate.
20XX and 20XXI: Youmu, Cirno, Daiyousei, Remilia, Wriggle, Reisin, Shinki, Alice, Marisa, Sanae, Suwako, Flandre, and Eirin.
20XXII: Yuugi, Keine, and Ran's babies are revealed to have passed away and Aya dies some time during.
20XXIII: Meiling and Patchouli, along with Seija in a Karmic Death
20XXIV: Sakuya, Reimu's mother, Ran's babies (save Yume Ni and An). As of chapter 50 in Gensokyo 20XXIV, some of those characters were brought back from the dead, through Yukari bending some of the borders of time to bring some of them to the future.
20XXV: Koishi, Satori, Yume Ni, An (being revealed to be Dead All Along), and, apparently, as of chapter 109, Ren. Along that line, it is implied that Yuuka has passed away and, by the 120th chapter, Kosuzu is mentioned to be "long gone", implying that she had died a long time prior.