Aang - Old Age
Agent Texas - Deleted by an EMP and later had a copy of her deleted from Epsilon's memories
Alex Mercer - Consumed by James Heller
Amuro Ray - Sacrificed himself by overloading ν Gundam's Psycho-Frame construct, caught in the explosion
Bayonetta - Soul forced out of body after being attacked by Gomorrah, soul dragged to Inferno
Bill Cipher - Existence deleted after being trapped in a mind that was getting its memories deleted
Cole MacGrath - Killed in the RFI surge
Darth Vader - Fatally electrocuted by Palpatine
Deathstroke - Fatally injured by Nightwing after the super soldier serum in his body was removed, put on life support before an unknown person pulled the plug on him
Dimitri Alexandre Blaiddyd - Passed away from illness
Dio Brando - Stand destroyed by Jotaro Kujo, body later left out in the sun to by burnt
Doctor Fate - Kent Nelson's body was turned to dust after he concentrated all his power into a blast that hurt the Upside-Down Man. Helmet of Fate and Nabu still live on
Doctor Wily - Unknown, most likely old age
Dracula Vlad Ţepeş - Slain in combat by Julius Belmont, Alucard, a Belnades, and the military
Epsilon - Sacrificed himself by fragmenting his body in order to run the M374 Hephaestus Combat Suit
Esdeath - Stabbed by Murasame, killed herself by freezing her body then shattering herself upon realizing that she had been defeated
Ganondorf - Slain by Link upon the Demon Dragon's defeat
Geese Howard - Fell from the top of his building a second time; still alive in the King of Fighters continuity though
Goku Black - Erased from existence by Lord Zeno after fusing with Future Zamasu
Heihachi Mishima - Killed in combat with Kazuya, body dropped into a volcano
Heracles - Burned off his mortal form after being in sever pain from his skin being coat in Hydra Poison
James Bond - Caught in a missile explosion
Jason Voorhees - Disintegrated upon being pushed through Earth II's atmosphere by Elijah Brodski
Jiraiya - Drowned after fatally wounded body was pushed into water
John Wick - Shot to death after the third round of his duel with Caine
Jonathan Joestar - Bleed to death after his throat was pierced by Dio's Space Ripper Stingy Eyes
Jotaro Kujo - Head bisected by Enrico Pucci
Leonard L. Church - Deleted after being caught in an EMP
Lucy - Mercy kill gunshot wound to the head after losing control of DNA Voice and body melting uncontrollably
Luke Skywalker - Over exertion after projecting an image of himself across several galaxies
M. Bison - Body destroyed after being hit a Hadoken from Ryu
Madara Uchiha - Killed after having the tailed beasts and Demonic Statue removed from his body
Magneto - Heart pulled out by Uranos
Makima - Body chopped into piece and turned into a buffet in which Denji consumed
Mega Man - Unknown
Mega Max X - Body destroyed by Elpizo
Michael Myers - Bleed to death after having both his wrist cut open...(Pretty lame for an unstoppable killer), later had his body pushed into an industrial shredder
Obi-Wan Kenobi - Allowed himself to be struck down by Darth Vader in their final battle
Obito Uchiha - Sacrifices himself by shielding Naruto and Kakashi from Kaguya's attack
Omni-Man - Killed by Thragg in their battle
Phoenix - Stabbed through the chest by Moira while trying to shield guests from an ambush by Orchis
Portgas D. Ace - Hole punched through him by Akainu while protecting Luffy
Ragna the Bloodedge - Walked into the Gate, recreating the world without anyone having memory of his existence
Randy Savage - Atherosclerotic heart disease
Reverse-Flash - Erased from existence by Barry Allen resetting the timeline
Sailor Galaxia - Literally by friendship, bracelets shattered after losing the will to fight against Sailor Moon's purity, hope, and love
Satoru Gojo - Bisected by Sukuna's Mahoraga
Sauron - Physical body destroyed upon the destruction of the One Ring
Senketsu (I'll count him) - Burnt up in the atmosphere protecting Ryūko
Sephiroth - Physical and mental presence defeated forcing him to reside in the Lifestream, for the being
Sigma - Body destroyed by X, Zero, and Axl, lacked new any new bodies to transfer to
Sindel - Impaled by a katana used by an alternate version of herself, soul taken in by Ermac
Sweet Tooth - Suffocated in a coffin after being tricked by Calypso
Tanjiro Kamado - Unknown, most likely natural causes
Tetsuo Shima - Exploded after being overwhelmed by his power, recreating the universe in the process
Thanos - Sucked into a blackhole, body could not resurrect properly later and was destroyed again by failsafe created by Druig
The Meta - Several puncture wounds in his suit lead to him drowning after being dragged into the ocean due to a warhog being pushed over a cliff while had its cabal attached to his chest plate
The Scout - After dying for a short period of time, god explained that he'd die again on December 4th, 1987
The Terminator - Many versions of these models of died, so its a tad bit difficult to say it has a real death scene since there should be more out there. But, presumably when Skynet gets shut down, all production of T-800/850 get shut down as well
Yellow Ranger - Died after taking Robo Rita's blast
Yoda - Old ass ************ died of old age
Zero - Killed upon crashing the space station Ragnarok