Here is a list of Nemesis's belonging to many comic characters. Enjoy.
STARFIRE
Blackfire
HAWKMAN
Shadow Theif
RAVEN
Trigon
DOOM PATROL
Brotherhood of Evil
BATMAN INC.
Leviathan
THE BATMAN
The Joker
NIGHTWING
Tony Zucco
BATGIRL
Hard to say. Knightfall, Jim Gordon Jr., Killer Moth, Firefly and The Joker all come to mind.
RED HOOD
The Joker
SWAMP THING/ANIMAL MAN:
Antone Arcane
JUSTICE LEAGUE
Darkseid (Who is pretty much the main baddie of the DCU since the New 52) and Crime Syndicate
JLA(NOT THE SAME THING AS JUSTICE LEAGUE SINCE NEW 52)
Secret Society of Supervillains
THE AVENGERS
Thanos, Kang the Conqueror and Ultron all fit this category
SILVER SURFER
Galactus
FANTASTIC FOUR
Dr. Doom
JESSICA JONES
Purple Man
SPIDERMAN
Norman Osbourn
AQUAMAN
Black Manta
THE FLASH
Reverse Flash. Due to the fact there are several Flashes, each has their own Reverse Flash:
Barry Allan has Professor Zoom, Wally West has Zoom, Jay Garrick has The Rival, Bart Allan has Inertia and New 52 Barry has Daniel West.
Also, Captain Cold (leader of the Rogues) fits this role when the Reverse Flashes are absent. In the 90s TV show, the Gameboy video game and many other Flash adaptations, the Trickster is often portrayed as the main bad guy.
SUPERMAN
Lex Luthor
DAREDEVIL
Kingpin. Bullseye (2nd).
JUDGE DREDD
Judge Death
BLACK LIGHTNING
Tobias Whale
IRON MAN
The Mandarin
NINJA TURTLES
Shredder
INDESTRUCTIBLE HULK
Leader. Abomination (2nd)
WONDER WOMAN
Ares, Circe and Cheetah fit this description
PUNISHER
Jigsaw
JONAH HEX
Quentin Turnbull
CAPTAIN AMERICA
Red Skull
THOR
Loki
FIRESTORM
Killer Frost
X-MEN
Magneto
JOHN CONSTANTINE
Cult Of The Cold Flame
GHOST RIDER
Mephisto
BLADE
Decon Frost, though an argument can be made for Vlad Dracula (Marvel)
GREEN LANTERN
Sinestro
SHAZAM
Black Adam and Dr. Sivana both fit this category
METAMORPHO
Simon stagg
CYBORG
Ron Evers?
RUNAWAYS
The Pride
WATCHMEN
Ozymandias
GREEN ARROW
The Dark Archer
NICK FURY
The HYDRA organization
WOLVERINE
Sabretooth and Weapon X
SUPERBOY
CADMUS (Pre-New 52); NOWHERE (New 52)
SUICIDE SQUAD
Basilisk
ANTI-VENOM
Symbiotes
SPAWN
Violator
BLACK PANTHER
Ulysses Claw
STATIC SHOCK
Ebon
DR. FATE
Wotan
MARTIAN MANHUNTER
Ma'alefa'ak
ZATANNA
Brother Night
LUKE CAGE
Hard to say. Purple Man and Chemistro come to mind.
IRON FIST
Master Khan
TEEN TITANS
Deathstroke
PHIL COULSON'S AGENTS OF SHIELD (Marvel Universe Earth-199999)
Centipede Organization and their yet-to-be revealed Clairvoyant (and I doubt it's Marvel's Claire Voyant)
CABLE
Apocalypse
EARTH-2
Darkseid
NEW GODS OF NEW GENESIS
Darkseid
INSURGENCY (Injustice: Gods Among Us Universe Earth V)
Superman's Regime
ROBIN
Some Encyclopedia's, magizines, ETC list Two-Face as Robin's arch enemy
BATWOMAN
Alice
BLACK BOLT
Maximus
HOWARD THE DUCK
Dr. Bong
HUMAN TORCH
Inhuman Torch
HELLBOY
Ogru Jahad
ATOM SMASHER/APACHE CHIEF
Giganta
STARMAN
The Mist
DR STRANGE
Dormammu
DEADPOOL
T-Ray
MOON NIGHT
Bushman
HAWKEYE
Crossfire
ADAM WARLOCK
Thanos
BATMAN BEYOND
Blight
MS MARVEL
Moonstone
GUARDIANS OF THE GALAXY
Ronin The Accuser
AMADEUS ARKHAM
The "Mad Dog" Killer
VAMPIRELLA
Vlad Dracula (Not to be confused with characters of the same name from Marvel and Bram Stoker. They all draw inspiration from historical figure Vlad The Impaler)
ANT-MAN
Egghead (not to be confused with Batman villain of the same name)
ADAM STRANGE
Kanjar Ro
SENTRY
The Void
CAPTAIN MAR-VELL
Yon-Rogg
SUPERGIRL
Brainiac