Clock Tower is pointed to by many as one of the scariest video game series ever, and these examples prove that point quite well.
Spoilers abound below. Beware.
Clock Tower on the SNES is absolutely disturbing. The constant fear of the Scissorman ambushing you eats at one's nerve. But worse, finding your friends dead in the worst of places, like trapped in a suit of armour. Then there's the demonic fetus baby, which is on a level all its own. Throw in that all but a couple of endings result in you being killed later on anyway, and you've got a twisted game.
To elaborate on the bad endings in the SNES version:
You run into an elevator, and the doors close just as you find out that Bobby is in there too. It stops mid-transit, you hear Bobby's laughter, and he then drops down into the very small, very enclosed space with Jennifer, scissors at the ready. Cue Jennifer screaming, that horrible sound of Bobby's scissors snapping, and a huge pool of Jennifer's blood oozing out under the door.
It seems like Jennifer has survived the nightmare. However, the very end of the text epilogue reveals that she was mysteriously found dead in her bed very soon afterward.
After eliminating Dan, Jennifer finds Mary and, oblivious to Mary's true nature, runs up to hug her out of relief. Cue Jennifer getting stabbed in the chest and pitifully asking "Why?" before collapsing.
So many of the friend deaths in the first game. The pool drowning, shower, and throwing from the clock tower take the cake. Lotte's death is either the also-creepy sacrifice, or the Crowning Moment Of Awesome that is saving Jennifer's life, which unfortunately isn't canon. And according to Word of God, Laura's death was due to her running to the phone to call 911. Somebody was waiting there.
The trophy room in the first game. Not just the room itself, with the bizarre sounds coming from the walls. You also find a human heart in a jar, which is still beating. And do you want to know who that belongs to? The mummified corpse that you find in the locker in the same room. Which, in some versions of the game, opens its horrible looking eyes, gets up, and tries to kill you.
You thought Scissorman was scary? Believe me, you will shit bricks by the dozen when you finally meet the titular Ax-Crazy psycho of Clock Tower: Ghost Head. Imagine this: You're all alone in a room, trying to find a piece of a puzzle or your amulet that will let you switch personalities, and all of a sudden an Implacable Man in a bloody lab coat and Hannya mask dragging around a giant machete barges in. Cue chase sequence! It's a lot more startling than it sounds, especially since you have no idea when it'll happen; at least with the other stalkers you usually get a Musical Spoiler before having to deal with them. Then there's the scraping...
And let's not forget the way the environment tries to kill you. You can walk into a room and suddenly have the floor fall out from under you, or have a porcelain doll rise from the floor and dash at you, or have a disembodied hand jump out through the mirror and strangle you.
Dan. Just Dan. Creepier when you realize that, according to the second game and Word of God, he's somewhat of a well-meaning, but still evil being. And the "fetus" form he took in the first game? Just a shell made of the corpses of the previous victims.
The body you can find in the sealed room. It's actually the body of Jennifer's father, a doctor who was called to help with the boys' birth, only to get his right hand eaten. He was then sealed off in a room to die from suffocation because he knew too much.
The second game has numerous death scenes for some of the characters once you reach Barrows/Burroughs castle. One character, Beth, is found dismembered inside a wine barrel on Jennifer's route, and is yanked through the floor on Helen's route. Another character, Tim, is found stuffed inside the chimney on Jennifer's route, and has a death remarkably similar to Beth's on Helen's route. You can also find Harris's head in a pot in Helen's game, find Barton hung from a tree on Jennifer's route, and find Gotts trapped inside a torture gear in Jennifer's game. There's also the suggestion that if you fail to release Nolan from the coffin in Helen's route, or Helen from the box in Jennifer's route, they were left inside and suffocated in there.
According to an interview with the original creator (posted on the Remothered fanpage on 1/4/2010), the Scissormen were originally from some sort of Hell "that cannot be perceived by the limited human cognitive system". The Scissormen are officially Eldritch Abominations.
At first, Mary seems like a sweet and maternal lady. That is, until you discover that she gave birth to Bobby and Dan. In one of the endings, you can find Mary upon returning to a room you've already been in. And she's just...standing there, with her hands pleasantly clasped behind her back. Then, all of a sudden, she pulls out a knife and starts walking very slowly toward Jennifer. It's easy enough to escape from, but...
Clock Tower 3 has more constant fear of ambushing, and surprise attacks to make you scream and jump out of your chair. Besides that, there's the extremely disturbing scenes of Sledgehammer killing a little girl, and Corroder giving a man and his mother an "acid bath".
The soundtrack helps add to the creep factor, such as the two Scissorman chasethemes. When either of these kicked in after the relative silence and lack of music in the game, you knew you were in some deep shit and had better find a hiding place as soon as possible. The second one was used more as a jump-out-at-out type of scare, but the first one is arguably more frightening because it's the one that just starts up randomly after you've simply walked around for a while without encountering him, so you don't know exactly where he might be. And for that matter, the chase theme from the original game for the Super Famicom (released only in Japan, but there is a fan translation available) is just as scary.
The shower scene in the first game, which may be the first scary scene you encounter. It's the one that shows Laura/Rolla tied up to the shower head, which is disturbing in and of itself, but then the Scissorman bursts out of the bathtub with his scissors opened wide. This scene is in first person, played to a horrifying musical sting, and has Jennifer's portrait zooming in on her eye to express her own shock at Scissorman's appearance.