Mephisto - Blackheart, Mephista
Sebastion Shaw - Shinobi Shaw
Justin Hammer - Crimson Cowl
Piledriver - Excavator
Abomination - ?
> Mastermind - two daughters: Mastermind (Martinique Jason) and Lady Mastermind (Regan Wyngarde)
Attuma - Andromeda
Lyra - Lyron
Puppet Master - Alicia Masters
Normon Osborn - Harry - Normie
Kingpin - The Rose
Mandarin - Temugin
Red Skull - Sin
Magneto - Quicksilver- Luna, Scarlet Witch -the twins(Speed,Wiccan?)
Venom symbiote - Carnage -Toxin
J Jonah Jameson(technically villain) - John Jameson
Spencer Smythe- Alistair Smythe
Sabertooth - Graydon Creed
Baron von Strucker - Fenris twins
Mystique - Nightcrawler, Graydon
Kand - Marcus
Umar - Clea
Unus - Uniscione, Radius?
Mad Thinker - ?
Tinkerer - The Agent - grandson?
Baron Zemo - Baron Zemo
Loki - Hela?
Dr. Doom - Kristoff(adopted)
Thanos - Gamora(adopted), possibly Nebula
Annihilus - the baby
Blastaar - Burstaar
Count Nefaria - Madame Masque
Kraven - Grim Hunter, Al Kraven
Ultron - Vision, Jocasta
I seem to remember that old Spidey villain Big Man had a daughter... who also became Big Man.
And didn't the Crime-Master have a son?
Come to think about it, the Burglar had a daughter that appeared in some later portions of Clone Saga...
And does Seward Trainer count as a villain? He was the father of female Doctor Octopus.