Sonic Characters So far

Heros
Sonic the Hedgehog (BOOM!)
Sonia and Manic (TV Show. Sonic Underground.)
Sonic the Hedgehog (Classic)
Miles "Tails" Prower (Modern)
Caliburn (Sonic and the Black Night)
Amy Rose (Modern)
Amy Rose (BOOM!)
Silver the Hedgehog (Sonic '06)
Jet the Hawk (Sonic Free Riders. Sonic Zero Gravity.)
Knuckles the Echidna (Modern)
Knuckles Echidna (BOOM!)
Bunnie D'Coolette (Archie Sonic)
Bunnie D'Coolette (Archie Sonic Post Genesis Wave)
Antoine D'Coolette (Archie Sonic Post Genesis Wave)
Cream the Rabbit and Cheese the Chao
Sticks the Badger (Sonic BOOM!)
Big the Cat and Froggy
Cosmo the "plant-alien-thing" (Sonic X)
Sonic Man (Looks like Archie version, but is the Sonic '06 version.)
Professor Pickle (Sonic Unleashed)
Chip a.k.a. Light Gaia (Sonic Unleashed)
Blaze the Cat (Sonic Dash with memories of '06.)

(Mr.S/Wolf Sonic/Sonic(Modern)) and Sonata (Suit wearing Sonic with a Werehog form and mobian pony Sonata Dusk)

New Knothole Mobotropolis
Princess Sally Acorn/Sal (Archie Sonic)
Princess Sally Acorn/Sally (Archie Sonic Post Genesis Wave)
Nichole (Archie Sonic Post Genesis Wave)
Rotor Walrus (SATAM Sonic)
Rotor Walrus (Archie Sonic Post Genesis Wave)
Charmie Bee (Archie Sonic)
Vector (Archie Sonic)
Mighty, Ray the Squirrel, and Bean the Dynamite (Archie Comics)

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Bad Guys
Time Eater (Sonic Generations)

Time Sombra (King Sombra spirit + Time Eater being (Sonic Generation)) / Solar Sombra(?) (King Sombra + Solaris (Sonic '06)) / Solar Time Sombra(?) (King Sombra + Time Eater + Solaris)
-Rosey the Rascal (Archie Sonic. Alternate Universe Amy.)
-Scourge the Hedgehog and Anti-Sonic (Archie Sonic)
-Metal Scourge army (Archie Sonic)
-Erazor Djinn (Sonic and the Secret Rings)
-[Aria Blaze and Starlight Glimmer]
-Master Zik and his Zeti "the Deadly Six"

Robotnik Council

Dark Gaia(?)

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Neutral
Rouge the Bat

Shadow the Hedgehog (Looks like King Shadow from an Archie Sonic spinoff)
-Shadow the Hedgehog (BOOM!) - King Shadow's Advisor
-Shadow Army
-Misfit Shadow Soldiers

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Robotnik Council
Dr. Ivo Robotnik "Big Mouth" (Sat AM/Underground) "Beach Ball" (Classic)
Dr. Eggman "Loki" (Modern) "King" and "Racer" (Free Riders/Zero Gravity (2)) "Real Man" ('06.)
Dr. Eggman Nega "Nega" (Sonic Dash)

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Minions
Decoe, Bocoe, and Bokkun (Sonic X)
Orbot (Unleashed - Now)
Cubot (Colors - Now)
Scratch and Grounder (The Adventures of Sonic the Hedgehog)

Shadow the Hedgehog clones (Shadow's army. Sonic Heros. Shadow the Hedgehog game.)

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OCs / Secret Characters
Metal Sonic (Regular Metal Sonic with extra tech, low level magic, green wings with light green tips, and bright blue stripes along his head. He has a gem that resembles the element of magic and the powers of the Roboticized Masters including the "Sonic Shot". Has an avatar hologram that resembles Sonic with red eyes and green wings and stripes.)
-Nichole (She too has green wings and all of her black details are green. She rests in Metal Sonic's right ear and is suppressing his inner rage and boosting his sense of free will. Her prison is her best friend in a way.)

Nack the Weasel/Fang the Sniper (His gun is enhanced by the magic in the air and he can some-what fly.)

(Mr. S / Wolf Sonic / Sonic (Modern)) and Sonata Dusk (I give up. It's Sonic the Werehog (Sonic Unleashed) and his other world assistant time traveling like Doctor Who!) Let's assume Mr. S is wearing this in blue with a bigger coat and hat at night.

Sally Acorn (Which one? Both Archie Sonics.)

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Important characters that might appear.
Queen Aleena (Sonic's mom. Sonic: Underground)

The rest of the round table knights.
The rest of the Babylon Rouges.
Blaze the Cat
Breezie the Hedgehog (Sonic Archie. Might make her Comedy Chimp's rival.)

Ben "the Mutt" Muttski and Muttski (The first one is new world Muttski, mobian dog and apprentice to Uncle Chuck. Second one is old world Muttski, Sonic's pet dog. Both from Archie Sonic comics.)

Chaos (and Tikal?)
Mephiles the Dark (and Iblis?)
Black Doom

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Enemies
Eggman / Robotnik council
Roboticized Natives

Dark Gaia minions
Changelings (and Queen Chrysalis?)

Ibis minions (maybe. thinking about it in case of dragon chapter or Nega encounter)

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Bosses / Defeated Bosses
Time Eater (Sonic Generations)
Time Sombra

Alicorn Amulet Egg Dragoon (Egg Dragoon is from Sonic Unleashed and Sonic Generations)
Tom (MLP FiM. Tom the boulder that covered the mirror clone pool)
Time Sombra - 1
Warrior Sombra spirit - 1
Young Master Zik
Erazor Djinn - 1

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Honorable Mentions
Dr. Ivo Robotnik "Pingus" (From the Sonic the Hedgehog cartoon that features "Sonic Says")
Shard the Metal Sonic (Archie Comics. Original Metal Sonic, becomes good with upgrades.)
Bark the Polar Bear (Archie Comics. Silent boxing Polar Bear.)