Captain America I
citizen V I
Captain Marvel I
Captain Marvel III (Genis)
Vision II (Wanda's ex)
Moondragon (though I think she's coming back if she hasn't already)
Marvel Girl I
Ms. Marvel I (PROBABLY faked death)
Sersi (last I checked...she MAY be back)
Human Torch I
Miss America (can't believe noone has made a legacy for her)
Union Jack I
Goliath III (Bill Foster)
Thanos (Yah right)
Baron Zemo I
Black Knight II
Swordsman III (Von Strucker)
Andrea Von Strucker
Angar the Screamer
Mr. Sinister (yah right)
Kraven the Hunter I
Frederich Von Rohm
Stonewall (not really a villain)
Super Sabre (not really a villain)
Basilisk (forget all the other z-listers Scourge killed)
Steven Lang (back as a techno-zombie)
Bolivar Trask (see Steven Lang)
Graydon Creed (see Bolivar Trask)
The villains with Nitro at Stamford CT in Civil War
Red Guardian I
Hyperion (Squadron Sinister)
Rachel Van Helsing
It's hard to classify Vision as dead. The current Vision has the "original's" memory. Even Marvel.com
lists them as the same character.
Moondragon is back in GOTG.
Alpha Flight members are tricky, since there are duplicates of them out there in space.
Sersi is back, was in the Eternals series.
Aquarian is alive.
Caliban is back as techno-zombie.
Meltdown may still be alive. The story isn't finished, and time travel is involved. The writers have teased that she might not be dead.
Cypher appears to be coming back.
Owl is alive, just came back in Daredevil.