My personal most disgusting one is SCP-835, one of my favorites. Second is SCP-3003.
I thought of SCP-1545 at once just upon reading the title.
(Read this tale if you didn't get the point: Cleaning Larry)
Will add on more if I remember them
There are more things in heaven and earth, Horatio, than the dreamt of in your philosophy. —Hamlet 1.5
I would agree the "He's just taking a nap" one was spooky to me, and i didnt even try to attempt to understand Cleaning Larry.
SCP-3486, SCP-1782 (and, to a lesser extent, the rest of Holy Science), and SCP-2030 ("Cephalopods"). See a theme?
Surprised nobody has mentioned SCP-4231.
Perhaps others don’t feel the same way. There’s no particularly scary monsters, and while there’s some gore, there’s nothing that relies too heavily on traditionally "creepy" imagery.
But I felt sick the whole day after reading it. Emptiness, nausea, disgust-all things that bubbled in my chest and gut for a long, long while.
I think it’s because, anomalous, reality-bending phenomena aside, it felt…real. As in, these are things that actually happen to real people. There are no horribly deformed, mutated monsters under your bed, but there are godawful people that abuse, exploit, and assault other people out there in the world. And that terrifies and disgusts me far more than anything else.
Because 835 has already been invoked, I want to plug my underrated disgusting favorite from series I, SCP-400. The one with the pillbug colony and infants.

i forgot the number but a cup of joe

SCP-590 They use someone with a mental capacity of a 3 year old to cure agents, and he gets their disease or injury. What's more horrifying is that he was never given a name, just 590. He can't go out of containment or form any kind of relationship with anyone. Truly dark.
"The Flesh that Hates", gods that one gave me nightmares for a week the first time I read it. Truly disgusting and eerie with how easily the world could end if this disease were to escape.

Staff notice: this user has been permanently banned for sockpuppeting and ban evasion.

I suddenly changed my mind about 590 this is some truly dark shit.