It's been a long time since Season 3 on Supernatural. Sam and Dean almost seem like different characters. Dean has become more serious, and Sam has become more confident. Their older/younger sibling relationship also changed as both seem to respect each other even more.
However, in Season 3, the stakes were getting to be high. At the end of Season 2, Sam had been killed and resurrected. Dean promised his soul to the crossroads demon in order to bring Sam back. He has one year to live. Additionally, Sam deals with having demon blood in him. He befriends Ruby, a demon who appears to have a conscience (appears being the correct word). Never to disappoint, Season 3 delivers truly scary scenes.
10 The Old Sewn-Up Surgeon: Episode 15
Desperate to find a cure for Dean's imminent death, Sam considers the methods of an old doctor, Doc. Benton. The doctor became crazed with finding immortality. In a way, he does, by taking organs and other essential body parts from other people and putting them into himself.
Taken by the scary doctor, Sam has his eyelids taped open. Anything that threatens the eyes, feels downright scary.
9 Vampire Gordon: Episode 7
Gordon, an obsessed hunter, changes into a vampire. He wants to do one thing, and one thing only with his new power--kill Sam. While Gordon frightens in his intensity and refusal to see shades of gray, Sam creates the scary scene.
Sam beheads a new, juiced-up and strong vampire with his hands and a metal wire (no other weapon). Although Sam did this to save Dean, even he seems shocked about his ability. This suggests that the demon blood is still in him, and powerfully so.
8 Evil Santa Kills a Father In Front of Son: Episode 8
Sam and Dean investigate mysterious deaths around Christmas time. For the second death, we see more of it in action. An evil Santa pulls a father from his bed, kicking and screaming. Santa puts the father in a red bag and drags him down the stairs. In order to silence the father and made the job easier, evil Santa kills him in front of the man's young son.
We see all of this from the young boy's perspective. The soundscape is haunting, such as the slowed-down Silent Night carol placed in the background of this moment.
7 The Table of Dead Bodies: Episode 13
In an otherwise humorous episode (aka Ghostfacers!), we have one truly scary scene. The ghost they're hunting was very lonely and found odd ways to appease his loneliness in life and in death. The ghost had been a janitor at a local morgue who would take the bodies and play with them. As a ghost, he's taking live people, killing them, and playing with them--treating them like dolls.
Sam is taken, and he finds himself at the craziest table of birthday guests: dead bodies taken from the morgue, and one live guest (Corbett). The song lyrics, "It's my party. I'll cry if I want to," are on loop. We see the scene as if from a shaky camera. This means that the images around the table are dim, making them so much scarier.
6 Fairytale Old Lady: Episode 5
A young girl is in a coma and has been for years. In a sense, she's a living corpse, and her spirit gets angry that no one listens to her. Her angry manifests in a peculiar way: The fairytales that her father reads to her end up becoming real.
The scariest scene is when a brother and sister (i.e. Hansel and Gretel) stumble upon an old woman's house. Lost from their hike, the old woman offers them shelter and food. After eating the food (poisoned), the siblings fall to the ground. Our old woman smiles sweetly while she holds the knife, "Everything's fine. You just hold still, my dear." Fairytales are ripe for horror, and this scene proves the point.
5 Witches and Teeth: Episode 9
Episode 9 opens with what looks like a romantic evening between a husband and wife. After returning from a bad party, they decide to make a party of their own. The wife goes to freshen up. While she brushes her teeth, she notices something. One tooth falls out of her mouth, then more and more, until she's dies on the floor with a bloody mouth. While a scary scene, it was a great way to begin an episode.
4 Long Distance Call, "Come to Me:" Episode 14
In the middle of the night, a teenage girl chats online to what she thinks is her dead mother's spirit. We see the lines that they write each other. The mother says that she wants to see the girl. Ultimately, she wants the girl to kill herself. The teenage girl writes that she's scared, and the mother says that she is with her--not to be scared.
Then we see the mother's image reflected in the computer screen, reaching over to touch her daughter's shoulder. Rightfully so, the daughter is terrified, turns the computer off, and jumps back. But the spirit isn't done with her, it writes, "Come to see," multiple times upon the dark screen. We find out that the spirit is masquerading as the mother, but it's equally horrifying--the message that the spirit sends and the method, in which, it delivers the message.
3 Lilith and the Unfortunate Cat: Episode 16
When the demon, Lilith, wants to play, she possesses young girls and kills us their whole families. It's disturbing to see a young girl, presented as innocent, do something so terrible. Towards the start of this episode, we see an innocent blond little girl come downstairs in a dress smeared with blood. When her family asks what happened, Lilith (in the girl's form) says, "Freckles was mean to me."
This screen builds to another scene when Lilith easily takes out the grandfather at the dining room table. Both scary, but the dress smeared with blood wins. Lilith knows how to make an entrance.
2 Hell-Hounds and Dean: Episode 16
In the same episode, we have one other truly scary moment. Since the beginning of Season 3, we know that Dean's life has a time limit. We also know that he is bound to hell based on the contract he made with the crossroads demon in order to save Sam. As much as Sam has tried, he can't save his brother.
Lilith possesses the body that Ruby was in, tricking the brothers. Then, she lets the hell hounds in. We see Dean mauled to death by invisible forces, truly a terrifying moment.
1 Changeling in the Car: Episode 2
We could write a list of scary scenes just based on this episode, The Kids Are All Right. When Dean goes back to see an old flame (Lisa), he and Sam discover that odd and monstrous events are occurring in her neighborhood. Little by little, we learn that the actual kids in the neighborhood are being taken and replaced by changelings.
The changelings look like the kids, but they are intense and extremely dependent on the mothers (literally feeding off them). One of Lisa's friends, convinced that her daughter isn't her daughter, decides to drown her daughter by driving the car into a lake. As she drives to the lake, she looks in her mirror, and the true face of the child is revealed. That face is the face of nightmares.