Feels pretty good to see so much support for Suikoden 2's very own Luca Blight. To say he's not even close to being the final boss of the game speaks volumes on how much of an impact he makes.

To quote - "It took hundreds to kill me but I killed humans by the thousands!"

Kefka

I have to go with that and add that weird mask salesman.

Quite a few come to mind:

Donkey Kong - The first real villain.  You feel like you are battling King Kong on a skyscraper.
Mario - I love that they made Mario the villain in Donkey Kong Jr.  They don't do anything quite this bold anymore.
Metroid - The first time I really got scared in a video game was the first time I encountered a Metroid on the NES version.
Dracula - He's a great villain period, gaming or otherwise.  He's a villain that transcends any one medium.
Big Boss - Metal Gear on the NES was a decent game, but I really love the twist about who the real villain was.
Mike Tyson - When the NES Punch Out was released, he was the undefeated heavy weight champion.  On top of that he knocks you out with one punch.
Link's Shadow - After beating the final boss of the final dungeon in Zelda 2, you have to fight an even tougher boss: your own shadow.
Kefka - He may be the greatest villain on this list.  If you've played FFVI, then you know why.
Sephiroth - A villain to rival Kefka.  If you've played FFVII, then you know why.
Delita - FF Tactics has several great villains, but Delita may be my favorite.
Stan - Okage has only so-so gameplay mechanics, but the story and characters are awesome.  And Stan, the evil king, is the best of the lot.
GLaDOS - It's true.  This robot has a lot of personality.
Selvaria - She's the Valkyrie from Valkyria Chronicles.  She's invincible and you have to face her on the battlefield anyway.

Crapcom ? are u F serious ?

Quite serious. They have gone out of their way to screw over and neglect Switch owners basically every chance they get. That to me makes them a villain.

That said, my opinion is not set in stone; it's possible they could redeem themselves. Putting a proper Monster Hunter on Switch would be a good start.