Conda Challis. During his appearance as the notional villain of Orphan Star, he displays a truly legendary capacity for depravity. Among other things, he attempts to recruit Flinx to create memory-plays in the Janus Jewels, and the "scenes" he wants to see turn the stomach of even a hardened Street Urchin like Flinx. He loves torture as well, but the best example is what he plans to do with his "adopted daughter", Mahnahmi — raise her to maturity and then use her as a sex slave. It turns out that he was being telepathically manipulated by her much of the time, simply to keep him functional as a human being rather than descending into a vile pit of vice, which triggers his Villainous Breakdown when he discovers the fact.
Lord Dominic Estes Rose, a major villain in Bloodhype, is a drug dealer who trades in substances other dealers won't even touch, like the titular bloodhype. Like Challis, he enjoys torture, and responds to news of the escape of a set of captives by crushing some songbirds in a cage. He then attempts to blackmail the AAnn on Repler by threatening to release his stash of bloodhype in their compound, horribly killing all of them, and manages to provoke the AAnn commander into declaring him the most disgusting being he's ever seen. His hubris reaches its pinnacle when he attempts to sell humanity out to the Vom in exchange for his survival, and promptly dies.
Inferred Holocaust: Better hope nobody lives in the universe which Flinx dumped the Great Evil into at the end of Flinx Transcendent. Also, once the Great Evil has been dealt with, what will happen if the Xunca decide it's safe to return to their original galaxy and kick out the squatters?
Any time the effects of Pip's venom are described in detail. Eye Scream only begins to cover it.
There's a particularly memorable scene in Bloodhype when Dominic Rose crushes some exotic birds in a cage, plus the description of the effects of the drug itself.
Conda Challis' nasty little perversions in Orphan Star — although this is given something of a Gory Discretion Shot by only describing Flinx's reaction to (and Challis' pleasure from) them.
The planet of Midworld could be considered Nightmare Fuel incarnate given the enormously varied and nasty ways the plant life has to kill people.
There's a scene in Trouble Magnet when a part of the Street Urchin gang are tortured by having thousands of sharp pointy metal objects pinned to them via magnets.
In Dirge, the reveal about the true nature of the Pitar: on the outside, they look like extremely attractive humans with unusual skin and hair colours. In fact, the entire species is so narcissistic that they can't stand the thought of allowing other races to exist, so they intended to wipe them all out. However, they realised that they had a very obvious flaw: they produced children at a much slower rate than the other known races, so if they openly waged war on the other races, they wouldn't be able to recover any lost numbers at the same rate as their enemies. Their solution to this was to attack the innocent human colony of Treetrunk, kill everyone and eviscerate the adult women to steal their reproductive organs, which would be modified and used to help make more Pitar babies at a faster rate than normal. When the other races wage war on them, they're forced to wipe the Pitar out- not because they want to, but because the entire race refused to surrender and just kept fighting, even the children. Even the few rare ones captured alive either mentally shut down/go insane, or commit suicide.
The Woobie: Flinx's alienation from the rest of humanity is played for all the Wangst that it's worth and then some, especially in the later novels.