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.
Tomas Nau from A Deepness in the Sky leads The Emergents . As part of their defeat of the rival Qeng Ho, Nau rapes and murders their fleet commander in front of her daughter. Following that Nau has the daughter mind-wiped and charms her into falling for him. Because the mind-wipe is imperfect, every so often Qiwi remembers what happened, tries to kill Nau, who then has her scrubbed and starts the process again. This continues for decades.
Flenser from A Fire Upon The Deepgot his name from his first steps as an Evilutionary Biologist — vivisection. Later, after becoming a ruler, he went far, far beyond that, among other things essentially turning Mind Rape of his subjects into a semi-industrial process. Flenser is a heartless sociopath, who demands absolute loyalty from his underlings, but has none to them. To him, everyone is a tool, although he can hide that well until the time comes. He murders followers and discards even his trusted bodyguards without a second thought. His own second-in-command (who, as revealed later, was essentially his offspring as well) hated him more than anything in the world, but too mentally scarred to resist. His striving to take over the world seems almost not worth mentioning compared to his other aspects. The book gives many glimpses into Flenser's mind and about the only non-horrible thing there is his ability to enjoy the beauty of nature.
Vendacious from The Children of the Sky upholds the tradition of horrifically evil villains and maybe even surpasses his predecessors, if not in scale and inventiveness of evil deeds, then in sheer sadism and pettiness. This guy adopts most of the old Flenser's methods, such as manipulation, treachery, absolute ruthlessness, and totalitarian control through physical and mental torture. And uses them to pit the two greatest centers of civilization in the world against each other, when neither side has any real reason for conflict. Any justification for this, or grand goal behind this? Vendacious thinks that justifications are for the weak - he recognizes, that his actions are meant to stroke his own ego and enjoy the feeling of power, and is perversely proud of that. He deliberately makes his own underlings' lives hell, just to see with how much tyranny he can get away with.
Genius Bonus: There are subtle hints throughout A Fire Upon The Deep that Sjandra Kei, as well as much of human civilization in both the Slow Zone and in the Beyond, is a matriarchal society.
It is stated explicitly in Chapter Eight in a Fire Upon the Deep that Pham is from a male-dominated culture, unlike the rest of humanity - which Sjandra is surprised at, as 'virtually the opposite of the matriarchy that all Beyonder humanity descended from.'
Nearly every character's last name ends in -ndot. As in "Dottr" or "Daughter of," in keeping with Scandinavian naming conventions.
In The Children of the Sky, when Ravna asks Nevil about his parents' roles before the disaster, he makes a point of clarifying that his mother was in charge of the Straumer scientists, not his father.
As the "Age of Princesses" gets more and more mention, it becomes clearer that they are not just references to some generic, mythical medieval society that happened to have princesses, but an actual specific civilization from which most modern humans are descended, and which was centered around "the Princesses", presumably the matriarchal rulers. These references start to get much more explicit in The Children of the Sky.
Iron Woobie: Pham Nuwen. His highest dream was to make the Qeng Ho a permanent civilization and beat the limitations of the Slow Zone. Instead he was betrayed and his followers scattered across space and time. Dug out of the hole he chose to die in, he discovers Focus may make his dream possible - at far too high a price - and gives it up. Then he discovers, quite by accident, the Zones of Thought that would make his dream truly possible...and gets them backward, ultimately ending up a semi-automaton of a Power. He couldn't buy a break with all the archives in the High Beyond.
Tomas Nau: when we meet him he's already over the horizon by several million klicks — but it takes time for the truth to come out. If he hadn't already passed it before, we see several MEHs for him in text, but the biggest one is probably that he keeps Qiwi as a lover while still keeping around video footage of the time he raped and murdered her mother; then repeatedly allows her to find out about this and then wipes her memory of the event.
In The Children of the Sky, Nevil Storherte spends most of the novel coming across as a weaselly but charismatic manipulator, hungry for power. Not particularly violent; he is not apparently complicit with some violent kidnappings early on (that is, he's complicit with the kidnappings, just not with them being violent), and when violence is done for his benefit, it's generally shown to be Vendacious indulging his truly evil urges rather than acting on Nevil's orders. So all in all, the only real harm he does seems to be due to his his seditious actions, not any actual violence or violent orders. Then, quite suddenly, he fires an explosive Wave Motion Gun into a crowd of civilians in an attempt to kill one person who might be there. Later, he even blames—privately, suggesting that he actually believes what he's saying—his intended target for what happened.