These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ensemble Darkhorse: Despite the player being unable to save her, Lotte is the most popular of Jennifer's friends within the fandom. There's also the Scissor Twins from 3, who seem to be the most popular of the Subordinates.
From Ghost Head is Bates/Sho. Both are complete badasses, but Bates is also played by Roger Jackson, and he's the only voice actor in the game who has any talent.
Also, Gotts from the second game for both averting Police Are Useless and being the only character who takes being chased by Scissorman in stride. His best scene is when Scissorman appears, he calmly draws his gun and shoots him. Of course, he quickly discovers his bullets don't have any effect...
Hilarious in Hindsight: The first two games centered around a powerless protagonist, who could only flee from and perhaps temporarily trip up their foe. Back then, this was a pretty unusual idea for gamers used to shooting away all of their problems. Now?Not so much.
"The bad guys are making no effort to chase Alyssa. She can literally just walk out the front door and be done with things. She can thwart the entire evil plan of her grandfather by just hanging out in an arcade playing Street Fighter 3 for the duration of her birthday.
The entire plot hinges on Alyssa being too fucking stupid to just leave."
Macekre: The third game, Ghost Head is set in Osaka, Japan. They try to fit it in California in the localization, despite everything being so Japanese. The references to Japanese folklore were completely removed as well.
Moment Of Awesome: When the birds you freed earlier in the first game come to Jennifer's rescue.
Lotte's (sadly non-canon) Heroic Sacrifice to rescue Jennifer in the first game.
Most Annoying Sound: At least in Clock Tower 3. "Alyssa! Alyssa! Alyssa!" or "Oh ho, that's a nice trick! Oh ho, that's a nice trick!"
Nightmare Retardant: In 3. Sledgehammer is truly frightening but everything afterward is this. Maybe except Corroder because you do see him kill people in horrifying ways, yet he gets repelled in very goofy ways like being slammed by a toilet door.
Also, Anne, from the first game, gets some flak because one of her four lines has her teasing Lotte's nervousness shortly after arriving in the mansion.
The journalist in The Struggle Within has no place in the story line. The only reason he exists is just so you can trigger ending C, which is pretty much the same as B. He doesn't even provide exposition besides what you already know.
Chief Nurse Cook as well. She's literally there just so you can learn about zombies, and give you a shotgun if she's alive... except there is a spot that will always give you a shot gun. The game's plot would not made any difference if she is simply left out.
And on one last note: Shannon. She's the supposed rival of the main character who has nothing to contribute besides conflict that never really had a proper resolution. She killed herself before the side-plot of her wanting revenge on Alyssa got resolved.
Shannon is definitely a case of a mishandled character/subplot. Her subplot could have been generally heartbreaking if done properly, and she was meant to kill herself because Allen definitely loved Alyssa more, but They Just Didn't Care and she got a couple of boring scenes.
Scrappy Mechanic: The Struggle Within seems as if it was designed without guns in mind. It gets even worse when you play as Alex since the hit boxes to click on the zombies are really picky to where it is nearly impossible to finish unless you shoot each zombie in order of who walked in before the next. It also drags.
The standard gameplay in The Struggle Within somehow had reduced difficulty over all. The only real difficult part about it is hoping you saved your game before you get locked into any of the bad endings.
They Wasted a Perfectly Good Plot: As a lot of reviews point out, The Struggle Within/Ghost Head is just a ripoff of Resident Evil (although it didn't start out as such - Memorial Pharmaceuticals was innocent, and George Maxwell was the one who released the zombies). The story however had potential, but the developers decided to Mind Screw us by letting zombies take over the plot after the first scenario and never fully explaining the backstory.
Clock Tower 3 as well, the premise was good and arguably deconstructs the concept of Magical Girls. But due to bad writing, plot holes, and obvious budget issues, the game never got to shine.
Uncanny Valley: Invoked in the 4th game because you do see corpses, but also unintentionally invoked with the character designs.
Viewer Gender Confusion: Players sometimes confuse Lotte from the first game as a boy. Her walking sprite does depict her with a large chest, but it's easy to miss the scene where she does move at all.
The Woobie: Alyssa later finds out that her real father is George Maxwell, who went insane due to a lab conspiracy by her adoptive father and uncle to discredit him. Sharron, who is revealed to be her step-sister, has been neglected by her father and hates Alyssa with a burning rage. On top of that, the people she loved and cared for (except for Kathryn) and some people she met (except for Alex and maybe Cook and/or the journalist) are all dead by the end of the game.
Guilt Complex: "Everyone's dead, and it's all my fault... It would have been better if I had died." Then subverted.
When She Smiles: After the hell she's been through. There is only one cutscene where you can finally see her happy.
By time Alyssa reaches Philip's home, his son is either possessed before being dead or murdered, his daughter has been murdered (as well, both) by his younger daughter, Stephanie Tate, who is (also) possessed and tries to murder him, his wife, and Alyssa and succeeds in any of the first six bad endings. This is not even going into his role in the back story...