I'm sure everyone here has good ideas of the scariest ghosts in video games, but here are some picks from me.

Kackle from Donkey Kong Country 2:

Chases Diddy and Dixie through a creepy old house and laughs evilly if he catches them.

King Boo from the Luigi's Mansion trilogy:

He wants to trap Luigi and his friends in paintings for eternity.

The Chozo Ghosts from Metroid Prime:

They relentlessly ambush Samus and aren't easy to defeat.

The Pokemon Tower ghosts from Pokemon Red & Blue:

Always found them very unpleasant when I didn't have the Silph Scope.

So what are the scariest video game ghosts to you?

Fatal Frame/Project Zero is packed with creepy spectres, but I think the most terrifying of all are the mourners; not only do they look and sound scary but they can seriously mess you up and you encounter them in small spaces with nowhere to run.

The mother in Sweet Home on Famicom.

This is what she does to someone who went near the furnace her baby died.

This thread can be just Fatal Frame alone

Or Silent Hill.

All horrifying, some of which I didn't even think of.

Here are more from me.

Alma Wade from the F.E.A.R. trilogy:

She was that much worse as a ghost.

Lisa from PT:

Fuck Konami for cancelling this game.

King Boom Boo from Sonic Adventure 2:

Loves chasing Knuckles and jumpscaring him.

Poes from The Legend of Zelda: Twilight Princess:

Their design this time around says it all.

I liked your picks, especially Kackle. Running from him in a rollercoaster with a literal countdown clock on the screen is very unnerving. He also utters a bone-chilling laugh when you lose on the level

Donkey Kong Country 2 OST - Player Down Haunted Chase with Kackle's Laugh (youtube.com)

That butler from Luigi's Mansion scared me as a kid.

The Hym in The Witcher 3.

It's a parasitic entity that feeds the hosts guilt and makes them go slowly insane until they commit suicide. You can't directly see it, only on the shadow of the host and you have no direct way to fight it and that makes it terrifying. 

The ghost that comes after the botchling is put to rest is also pretty creepy. Although it's a good spirit that's helpful and not malevolent. 

To be honest, can't really think of any I find genuinely scary.

Well here are some more from me.

Bomb Boo and Bouldergeist from Super Mario Galaxy:

The insane look on their faces on top of following you regardless if you look at them.

Genuinely creepy, and when you damage him enough times you see his uvula, which isn't exactly pleasant.

Death Sword from The Legend of Zelda: Twilight Princess:

Like a scarier and more aggressive version of the game's Poe enemies.

The Sorrow from Metal Gear Solid 3:

Technically on Snake's side but his appearances are genuinely disturbing.