Marvel's Secret Invasion definitely fits this trope. In it, Earth is invaded by shape-changing, reptilian aliens called Skrulls — and some of the invaders have supplanted certain people on Earth. Even worse, there is so far no way to distinguish the impostors from the people they're impersonating. To make matters still worse, the Skrull impostors have gained access to Earth's most advanced technologies — and sabotaged a lot of it. And furthermore, it's been suggested in places that some of the people they have replaced are sleeper agents who don't know that they're Skrulls until they've been "activated" — you could be one...
If you're unlucky enough to live in Earth-2149, then... well, congratulations! Hiding is useless, since Zombie Daredevil is gonna find you with a Quinjet, in order to trick you into thinking he's there to rescue you! Good thing he just proposed such an idea... not that it makes the horror any more bearable, that is.
The Invisibles. Gods and angels exist, and they are not your friends. Demons are watching you through closed-circuit television systems, and God is being dissected in an underground lab.
Or, depending on your interpretation of the Gainax Ending, it could be construed as the precise opposite of paranoia fuel.
The Sandman: your bad dreams are living entities that can kill you if they so choose. The only thing keeping them under control is a vindictive, spiteful and petty godlike entity who can easily condemn you to hell, or fates worse still with ease.
And your adorable cat, stretching her claws in her sleep? Yeah, she's dreaming about a world where giant cats hunt and eat humans. If enough of them dream it, it may even become real...
This was used as a punishment in Hell for Edwin Paine, one of the 'young' Dead Boy Detectives— he was murdered and he awoke in an endless corridor. He began walking down it; soon, he became aware of a very menacing presence following behind him. He realized that if he confronted it at all— looking over his shoulder, breaking into a run— he would be destroyed utterly. Cue walking down a hallway in absolute, unacknowledged terror for a few dozen decades.
Hack/Slash. All those unkillable fiends you see on the big screen? They're REAL. And they will kill you just because they can.
The "15 Minutes" storyline in the latest rewrite of Genął. The less said about it the better.
The O.M.A.C. Project in the lead-up to DC's Infinite Crisis. The shadowy spy organization Checkmate has cameras everywhere on Earth. Anyone on the street could be one of their deadly O.M.A.C. cyborgs. Their leader, a psychic, can make you do anything he wants from any distance. And Brother Eye is always watching.
The mostly funny one-shot featuring Galacta, the daughter of Galactus, is ripe Paranoia Fuelif you think about it too much. That cute girl with the glasses you always see ordering lunch at the local cafe? She's a Physical God that is always hungry and is constantly suppressing the urge to eat you. You and everybody else. And she thinks of everything as food.
If Superman knows you well enough, he can identify your heartbeat from across the city. Sometimes, he can hear it from the moon. It's not as bad as it could be, seeing as it's... well... Superman, but still...
How about the little fact that this flying indestructible superfast juggernaut with the laserbeam eyes has absolutely NO resistance to the legions of mind-controlling psychopaths that infest your world?
If you're a teenager who gets along reasonably well with your parents (Like Karolina), the whole first Runaways series is this. No matter how nice your parents seem, they could be evil... and how would you ever know?
Speaking of the Runaways, in the Runaway/Young Avengers Civil War crossover, there's this gem. Imagine you're a teenage superhero. You decide to help another team. This leads to you being kidnapped and forced to watch as the boy you love gets sliced open and operated on, while you can hear and see everything, and can't do anything about it. This leaves you brokenly wishing that the man doing this will die, and you can escape this nightmare. All because you wanted to help...
Night of the Owls: You will never look at owls the same way again. "Beware The Court of Owls, that watches all the time, ruling Gotham from a shadow perch, behind granite and lime."
Death of the Family: Picture this... a Monster Clown has returned from a year-long, retrieved his own face, and wears it like a mask. He has always been unpredictable, but he's sticking to the shadows and leaving you to wonder when and where he's going to strike. Then he reveals that he knows your secrets, including your identity. Now you wonder if he's lying or if he's telling the truth. You know what he is capable of doing, and may have been on the receiving end of it yourself. He'll go after you, or he'll go after the people you care about most. If none of this makes you paranoid, then nothing will!
The Gigantic Beard That Was Evil: Everyone in Here is always paranoid about the idea of There. There eventually breaks through to Here in a way nobody would have suspected - through a man's facial hair. Rapid Hair Growth has never been so existentially terrifying.
ROM Space Knight: The entire premise of the book has ROM searching down Dire Wraiths, who wielded black magic, could shapeshift and furthermore had a disgustingly long tongue/drill-thing that could pierce skulls and suck out both the memories/personality and lifeforce of human victims, leaving behind nothing but a pile of dust and allowing the Dire Wraith to impersonate their victim flawlessly. All this for a child's action figure robot comic-book tie-in.