QUICK NOTE: I used CC's 2016 poll data to compile this list. What I found was that since there were about half of the people total, scores were skewed heavily in favor of the 2016 poll participants. To correct this, the games featured on CC's 2016 poll had their bottom half of characters relegated in favor of getting more of the older games into the mix. In total, that culled 25 entries from the list. After looking at the next 25 entries on the list, I filled in any pre-2016 characters from that selection. There were about 9 spots still leftover, which I went back and filled in with the top 9 2016 participants who got cut.
It's not an exact science, but it was the best way to get a selection from all of MS history.
But... here are your TOP 100 CHARACTERS!
MUSHROOM KINGDOM
Goomba
Magikoopa
DESTINY ISLANDS
Altair
Shadow
SEAFOAM ISLANDS
Chansey
Golduck
MIDDLE EARTH
Halbarad
Haldir
Pippin
Wormtongue
SKY PILLAR
Ampharos
Forretress
Toxicroak
MASS EFFECT
Harbinger
Kasumi
Legion
ARKHAM ASYLUM
Deadshot
Poison Ivy 1.0
Scarecrow
GREECE
Anna-Liza
Jaime
Monika
GAME OF THRONES
Davos Seaworth
Gilly
Oberyn Martell
Tyrion Lannister
SEASON FINALE
Nappa
HOGWARTS
Fenrir
Neville Longbottom
Peeves
Stan
Tonks
CONCLAVE
Deadpool
Moon Knight
Starfire
Queen Bee
Wolverine
Zod
DOCTOR WHO
Dorium Maldovar
Jack Harkness
River Song
HYRULE
Dampe
Eldin
Navi
Tetra
NAMES ARE HARD
Doge
Frenchie
Simba
The Star Worn By Verka Serduchka
Tommy Wiseau
Valley Girl
EXPECT THE UNEXPECTED
nobody!
ARKHAM CITY
Abraham Lincoln
Alfred
Batwoman
Mr. Freeze
Rorschach
Star Sapphire
White Rabbit
PRETTY SUPER VANILLA
HunCalFroYo
Karamel Sutra
Mint Chocolate Chip
Wasabi
BATTLE OF THE BANDS
Dr. Teeth and the Electric Mayhem
Robyn
Tove Lo
Whitney Houston
EON
Banette
Delphox
Dewott
Pikachu
Tyrantrum
Zoroark
#2016
Barbara Boxer
Elizabeth Warren
Ted Cruz
Tulsi Gabbard
LEAGUE OF LEGENDS
Amumu
Dr. Mundo
Gnar
Lulu
Malphite
Shaco
Teemo
ABRIDGED
Buu
Kawazu
Android 18
Future Trunks
Young Trunks
MEDEVAC ISLAND
Alexis
Debb
JT
Nadiya
NEXUS
Abathur
Azmodan
D.Va
Tracer
Tyrael
SUMMER OF SPOOKZ
Jennifer Check
Sam
Stay Puft