This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / The Last Angel
When she first steps aboard Nemesis, Grace is reminded of a talk she had with Allyria when they were little that gave her nightmare afterwards.
Allyria Whatís the difference between something thatís dead, something thatís sleeping and something thatís waiting?
Allyria What happens to you.
When the crew of the 'Bequeathed' first board 'Nemesis', there's a distinctive thumping sound that echoes through the entire wreck that makes it hard to sleep and that the light flicker in time to. A few chapters later, they find out that it's the ship's railguns' loading mechanisms working to load non existent shells into the dead guns. The ship is trying to kill them despite being effectively dead from their point of view.
Nemesis likes to use nanomachines and subsonics to make people hear voices. The effect produced is absolutely terrifying - especially since it first shows up in a man who's encountered her before and had the memory blocked, so it looks like PTSD - then it starts happening to other people.
Actually, pretty much everything Nemesis does to boarders qualifies. To quote a reader "Any sufficiently advanced psychological warfare is indistinguishable from a hostile paranormal."
Echo. She's chained, yes, but it isn't enough. Red One describes her as being everything the Compact fears about her, and getting worse every time they try to recreate her, thinking they got it right this time. Now consider that the Compact views Red One as the Devil and Red One sees herself as a necessary monster.
The Oshantan Ai. it went completely right. it did what it was made to do. it made them happy.
According to the compact/Principality =, anyway. there is occasional debate in the thread on what exactly lead to that situation.
The Naiads. No one who isn't Red One or Echo can even confirm they exist, ships just disappear in the regions where their songs are heard. What Red One and Echo know isn't reassuring at all: The Naiads are some kind of species of living or sentient starship. They HUNT starships and don't seem to consider anyone but themselves to be really alive - they call everyone else 'deadtone'. Red One has a pact with one group, but they really don't understand her or anyone else - the queen of that group thinks blowing up Rally would be a favor
A full Naiad 'migration' would be a serious threat to the Compact as a whole. It's not due for a few millenia. Think about that - the Naiads don't care about anyone else, kill for sport, and the galactic superpower is under existential threaten from them when they are most active.
The More you read about the Compact's History, the More you realise it started out as a United Federation of Planets-style alliance. the Details of WHAT started its decay qualify, as would its current policies by the standards of its founders.
There's one line that sums up Nemesis from the perspective of the Compact
"Humanities greatest achievement was its most unforgiveable sin"