The Dearly Departed

This is a list of some of the dead characters
Avengers - Hextrix, Iron Man (Tony Stark), Joules (Maeve Doran), She-Hulk (Jen Walters), The Vision, Warmachine (James Rhodes), Wonder Man (Simon Williams)
Brotherhood of Evil Mutants - Alpha the Ultimate Mutant, Mesmero (Vincent), Shadow King, Toad (Mortimer Toynbee), Unus the Untouchable (Gunther Bain)
Hellions - Bevatron (Fabian Marechal-Julbin), Empath (Manuel Alfonso Rodrigo de la Rocha - Replaced with an alternate reality version which is alive)
Horsemen of Apocalypse - Apocalypse (En Sabah Nur), Holocaust (William Rolfson)
Fantastic Four - Mister Fantastic (Reed Richards), Spider-Man (Peter Parker)
Friends of Humanity - Graydon Creed
House of Agon - Black Bolt (Blackagar Boltagon), Crystal (Crystalia Amaquelin), Gorgon Petragon, Medusa (Medusalith Amaquelin)
Lockjaw
Infinity Gems - Mind (Blue), Reality (Yellow), Space (Purple)
Infinity Watch - Moondragon (Heather Douglas)
Morlocks (Chicago) - Cell, Litterbug, Postman (David), Shatter, Trader
Mutant Liberation Front - Locus (Rayna Piper), Moonstar (Danielle Moonstar), Thumbelina (Kristina Anderson), Zero (Ambient-Energy Dampening Actualization Module Unit Zero)
Potentials - Cypher (Douglas Ramse), Jubilee (Jubilation Lee), Magik (Illyana Rasputina - confirmed Angel), Sunpyre (Leyu Yoshida), Wolfsbane (Rahne Sinclair)
The Pyremid - Gaia, Jonah, and hundreds of other missing children
Sentinels: Tri-Sentinel
Serpent Society: Eel (Edward "Eddie" Lavel)
S.H.I.E.L.D. - Multiple Nick Fury (There always seem to be more)
Skrulls - Maeve Doran poser, Tony Stark poser.
United States of America Government - American Steel
Xavier Staff - Sharon Freidlander
X-Men - Archangel (Warren Worthington III), Colossus (Piotr Rasputin), Iceman (Robert Drake), Livewire (Maeve Doran), Marvel Girl (Jean Grey), Rictor (Julio Richter), Rogue (Anna Marie LeBeau), Vulcan (Gabriel Summers), Cyclops (Scott Summers), The White Queen (Emma Frost)
X-Force - Boom Boom (Tabitha Smith), Cable, Canonball (Samuel Guthrie), Copycat (Vanessa Carlysle), Shatterstar (Gaveedra Seven), Warpath (James Proudstar)
X-Terminators - Wiz Kid (Takashi "Taki" Matsuy)

Known Survivors

Morlocks, Survivors (Chicago) - Angel Dust (Christina), Electric Eve (Eve)
Morlocks, Survivors (New York) - Caliban, Callisto, Marrow (Sara), Masque (Jack MacNaughton)