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 is a matriarchal society. One of which is the fact that nearly every character's last name ends in -ndot. As in "Dottr" or "Daughter of," in keeping with Scandinavian naming conventions.
Iron Woobie: Pham Newen. 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.
Moral Event Horizon: 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.