Some of the paintings in Mandus' estate qualify as this. Especially the pig lady.
Mandus lampshading in his journal:
"I cannot help but feel I am trapped in some great game, forced to undertake endless herculean labors for the promised reward of my darling children! "
"Another confounded fuse box. The fellow is thorough in his sabotage, if somewhat repetitive."
In the final area, Mandus remarks that he looks towards the system for answers, and the system replies "Figure it out yourself, simpleton." .
The pig mask's appearances, for some, border on Black Comedy. There's a point where it cuts the whole "suddenly appearing where it wasn't five minutes ago" routine and places itself behind an open door. Hi!
The place where the manpigs are stored, in the few moments when it's not a Tear Jerker. Especially seeing how they interact with each other or when they are having dinner.
One caged manpig rushes towards you, then comically slips on a pile of goo. He lands on his backside, then shuffles back to the corner, defeated.
And due to the weird lighting, another caged manping looks like he's...fapping.
The Engineer's boast at his hammiest moment is more than a little comical, intentionally or not:
The Engineer: My time has come! More pig! More pig!
Early in the game you head a phone ring. You pick it up, expecting something totally freaky and terrifying. What you get is... Well, freaky but not quite so terrifying. The person on the phone tells you, in no uncertain terms, "precious eagle cactus fruit... help us," then hangs up. Why? Well, it's never explained.
It's a reference to Aztec sacrificial rituals. The victims' hearts, to be precise, so it's supposed to be foreshadowing. (Though admittedly since most people wouldn't know the phrase, it doesn't sound arcane and foreign, just goofy...)
Throughout the game are maps of the entire facility, with cylindrical message displays over them that keep factory workers updated on current status ("Facility flooded; get to the sluice gates," etc). Towards the end, as you're Spanner In The Worksing your way down, The Engineer rewrites them simply to say: