The Obituary:
MARVEL
Doctor Doom
Minron
Castle doom was destroyed by Abolisher, as well as most of Latveria. It is assumed that Doom did not survive the explosion.
Doctor Octopus
Sapphire_Spider
Teleported to within Killer Crock's cell. After being defeated, he was used as a human battering ram to break down the cell door. Cause of death was multiple internal injuries as a result of the battery.
Hybrid
Comic_Book_Joker
Ripped apart by the Hulk at Fisk Towers.
Morph (Age of Apocalypse)
Feral Fallen
Sacrificed his life to bring back Rosie in Fellromen.
Pyro
???
Accidental Death. Died of blunt forced head trauma while fighting a group of heroes. Body was left at a Hospital.
Shocker
Minron / sapphire_spider
Captured by Gold Star with telekenisis, then killed by multiple stab wounds.
DC
Doomsday
Minron / sapphire_spider
Victim of one of X’s temper tantrums and spontaneously combusted.
Ventriloquist (I)
Comic_Book_Joker
Shot point-blank by Joker in Gotham City.
OTHER
Abolisher (The)
Sapphire_Spider
Slain by the Spectre. His heart was ripped from his chest and destroyed.
Boba Fett [Star Wars]
Minron / Comic_Book_Joker
His ship was destroyed in space.
Commissar (The)
Minron
MIA. Suspected that he was returned to his own demension.
Fuze (Duplications)
Madam Gossamer / Sapphire_Spider
One duplicate was killed by Reaper when he drained her of her blood and powers. Her form faded into a red light and vanished.
Another duplicate was killed by Abolisher when he used his powers on her to try and make Spectre upset. She died of internal burning. This duplicate was later brought back to life after Morph sacrificed himself to save her.
Hoshi
XPRiku / Sapphire_Spider
Turned into a solid marble statue by Doctor Strange.
Jester I
XPRiku
Blown up by Green Goblin with a pumpkin bomb at Oscorp.
Mugin
XPRiku / Sapphire_Spider
Killed by Hoshi in an unseen realm. His severed head was sent to his mother, Alcina, in a box. The rest of his remains is suggested to be scattered throughout her home.
Reaper (Duplications)
Sapphire_Spider
Nearly all of Reaper's Duplicate's have been destroyed by Supergirl via freezing, crushing, smashing, tossed into the sun, ripped appart, turned into a bloody pool, burned alive, exploded, etc....
A few Duplicates have been killed by the Black Lantern Crow, via breaking and scream.
Scarecrow
Comic_Book_Joker
Captured and killed by Ghost Rider with his Penatance Stare.
Slash
XPRiku / Sapphire_Spider
MIA. It's assumed that he was killed along with Mugin by Hoshi.
NPC