This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Dragon Age: Origins – Awakening
One of your party members is a spirit of the Fade that must possess a corpse. So basically you have an animated corpse, still with its old, grave injuries that killed the body, and soulless eyes. Try not to look at him too hard.
The Anders short story also has the line "To stay in the mortal realm, he needs a host, a body to inhabit for a lifetime, not a corpse which will rot out from beneath him", implying that he's still rotting. More slowly than an ordinary corpse would, granted, but he's still going to look worse and worse as time wears on (to say nothing of what he probably smells like). Bonus nightmare fuel for imagining how awful it would be for Justice should his body ever deteriorate too much...
The Architect doesn't seem that creepy at first — especially not when compared to The Mother. Then you notice the little things that seem "off" about him. That Nice Hat of his? It's actually part of his head. And his eyes... yikes.
The final part of the short sidequest "Adria's Plight." Anything can be made scarier with shrieking.
Made worse for Nathaniel, who knew her growing up and considered Adria to be like a mother to him.
Drake's Fall is even more unnerving than the Deep Roads. Imagine a desolate wasteland in the dead of night littered with the bones of long dead dragons. Then add the hordes of Darkspawn. Then add the Children. Finally there's the cherry on the terror sundae: being ambushed by a High Dragon.
At the end of the "Last of the Legion" quest, at the very bottom of Kal Hirol, you find the Broodmother pit. Just one of those things is bad enough, but three... Brrrr.
The Warden arrives just in the nick of time to save Sigrun from being carried off by darkspawn, something she mentions happened to all of the other women in her unit. Made far worse as it's implied she knows perfectly well what happens to women the darkspawn take prisoner.
The Blackmarsh questline, from the start to finish. Dark swamp with werewolves and Children lurking abound, coupled with multiple, eerie Veil tears. And in the middle of it there's an abandoned, overgrown village. The part in the Fade isn't that bad if you don't count the crypt, but when you return you have to fight a force of Revenants and Shrieks, and the less we speak about The Baroness' true form, the better.
For me the scariest part of the Blackmarsh were the Blighted Werewolves. Here are creatures already cursed, transformed into monsters and unable to control their violent rage. And then they get the darkspawn corruption, probably through eating them, leaving them twisted, mad and in constant pain. Killing them felt like doing them a favour. Plus some of them can just POOF out of nowhere and suddenly your uberpowered main (or your horribly, horribly underarmored mage) is pinned to the ground by an Overwhelm from a high-level miniboss...
The Children in their Gigerian glory are pretty damn horrifying: take a human baby, cross it with a giant maggot, giver it some sharp teeth and jagged claws, and you got yourself Children that at times during battle will grab fellow darkspawn or hapless NPCs, devour them whole and turn bigger, faster, and gooier (and more dangerous) as a result.
Let's consider for a moment the Architect's plan: an end to the Blights and freedom for the darkspawn from the control of the Archdemons. Sounds great, right? But there's one thing, one little detail, which the Architect leaves out in his stirring speeches desiring darkspawn freedom, and it's staring you in the face through the main quest and Sigrun's introductory adventure: broodmothers, the primary means of darkspawn reproduction. The Architect may want his people to be free, but do you honestly think any woman would volunteer for something like that? While darkspawn don't age, the Architect probably wouldn't allow his race to have no way of replenishment through accidents or other problems.
The fact that the Architect has a plan is nightmarish in and of itself. The Archdemons are bad, bringing darkspawn to the surface in hordes and giving them direction and strategic thinking. But it's still just one creature with a single, clearly-defined objective - destroy. The Architect has plans, and subordinates that are also capable of intelligent thought, speech, and commanding other darkspawn. The plans it has aren't entirely clear. At least with an archdemon you know what it wants to do. The Architect has goals beyond "break things."
And it's even more unsettling now that BioWare has revealed what the Architect actually is. If the Warden-Commander spared him and agreed to his plan, that means that the Hero of Ferelden has literally allied him/herself to one of the ancient magisters who became the very first darkspawn. And there are at least two more running free in the Deep Roads.