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 and, apparently, the entire ruling class of Emergents. It seems like Thomas Nau in particular is trying to collect atrocities the way normal people collect stamps. Rape, genocide, and slavery are his favorites, and the he has all sorts of futuristic tools to help him with all three.
The original Flenser and Steel from A Fire Upon the Deep, although both the new Flenser and the Steel remnant are actually good-aligned, due to the addition or subtraction of members of their packs - Tines function as group minds whose identities and personalities change with the composition of their packs.
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.