While most of the victims' bodies you examine are fairly mundane if they were stabbed or shot, cases involving women that were beaten or strangled will have very realistic looking bruises and cuts that are downright horrifying. Moreso if the bodies are naked.
In the intro for every case on the Homicide desk, a woman is seen in a secluded area before letting out a scream when she is attacked by the killer. In one particular scene, a victim can be seen tied up and dragged out of a car, whimpering and crying in fear. The kidnapper takes a tire iron and smashes her skull, causing her to let out a very high pitched scream of pain. Every smash the murderer makes has the woman's screams grow more and more quiet until she is completely silent. While everything is done without any light at all so you can't see the details, the sounds alone are more than terrifying enough.
The entire Black Dahlia case is just a very unsettling matter to deal with, almost going into a horror movie type deal.
When you hear the explanation on why the corpses of the victims of an arson case look like they're praying, I betcha you'll feel something in your stomach.
From Bad to Worse: While Phelps and company discuss the evidence, or lack thereof, one of the corpses crumbles. It's too much for even Biggs to handle.
If you want to make it worse, after checking the corpse, listen to this piece of soundtrack.
Ira Hogeboom: You said the house would be empty!
During the "Manifest Destiny" case in Vice, you inspect the Hollywood Post Office after finishing a shootout there...and find a wounded shooter who dies shortly after. The look in his eyes just as he dies... Yeesh.
Not as bad as the other examples, but hearing Jack's scream as he's run over by the bulldozer if you don't move fast enough is pretty shudder-worthy.
The penultimate war flashback. In the one before it, Cole sends a man, flamethrower-wielding Ira Hogeboom, to clear out a cave complex suspected to be filled with Japanese. While he does it successfully, it turns out that the cave complex was being used as a makeshift hospital, with several civilians in it. The game thankfully doesn't show too many of them burning, but it certainly shows enough to get the point across. The guilt and horror of this is what ended up causing Ira to go insane, and even then he seemed to already be losing his grip on sanity, as he needs to be held down by other guys while screaming and wailing.
"He's not so bad. He just lays on top of me and grunts for a few minutes. He's kind and he buys me nice things." As said by a twelve-year-old girl, speaking of a fifty-two-year-old man.
The DLC "Nicholson Electroplating" case in the Arson desk. The whole case revolves around a massive explosion at the titular industrial plant that destroys not only the plant, but most of the surrounding block, leaving Oakwood Ave in such a state that Biggs first assumes that it was an attack by the Soviet Union. While the main crux of the case involves investigating a seemingly mundane case of cross-corporate espionage, imagine the events of the case in the perspective of a normal, everyday citizen...