Friendship is Magic
Apple Bloom's Shadow | Ahuizotl | Arimaspi | Bugbear | Changelings | Chimera | Cockatrice | Dr. Caballeron | Diamond Dogs | Discord | Dragons (Dragon Lord Torch, Garble, Sludge) | Flim Flam Brothers | Gladmane | Grogar | Hydra | King Sombra | Legion of Doom (Queen Chrysalis, Tirek & Cozy Glow) | Mane-iac | Maulwurf | Mean Six | Nightmare Moon | Parasprites | Pony of Shadows | Puckwudgies | Roc | Sable Spirit | Shadowbolts | Snips and Snails | Sphinx | Starlight Glimmer | Svengallop | Tantabus | Tatzlwurm | Timberwolves | Vampire Fruit Bats | Windigos | Wind Rider

Equestria Girls
Dazzlings (Adagio Dazzle, Aria Blaze & Sonata Dusk) | Juniper Montage | PostCrush (Kiwi Lollipop & Supernova Zap) | Principal Cinch | Snips and Snails | Sunset Shimmer | Vignette Valencia | Wallflower Blush

Generation One
Arabus | Beezen | Bray | Catrina | Dragon Gang | Flores | Grogar | Hydia | King Charlatan | Lavan | Princess Porcina | Queen Bumble | Raptorians | Reeka & Draggle | Somnambula | Squirk | Tirek | Zeb

Comics
Accord | Bad Apple | Chupacabra | Cosmos | Mane Six | Nightmare Rarity | Princess Celestia | Pseudocorns | Rabia | Shadowfright | Swift Foot | Vampiric Jackalope

Films
My Little Pony: The Movie (1986): Hydia | Reeka & Draggle | Smooze
My Little Pony: The Movie (2017): Storm King | Tempest Shadow | Grubber | Storm Creatures

That quite a list. I wouldn't mind seeing their villain alter ego.

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Don't forget about the villains from the G1 comic:

G1 Comic Villains: The Big Villains
G1 Comic Villains: Minor Villains
G1 Comic Villains: The Lame

You forgot about

• Rough Diamond, the phantom jewel thief from the IDW comics.
• The other villainous group in that Power Ponies annual comic (will add their names later.)

You missed Rough Diamond from the IDW comics arc Manehatten Mysteries.