Captain Fraul's death in Lord Brocktree. He's swarmed by a bunch of spider crabs and then suddenly disappears from the story. Later on, Dotti and Lord Brocktree stumble upon his corpse in a tunnel, which had been reduced to a skeleton. That's right. Crabs turned a fully-grown stoat into a fucking skeleton.
Also from Doomwyte, Baliss the Slayer. Starts off as a highly effective silent killer. After getting a face full of hedgehog spikes, and said wounds become infected, the snake goes completely insane. For comparison, take Asmodeus, make him bigger, smarter, and generally more dangerous. Now make him batshit insane and blind. Not pretty.
The Freebeast's shipwreck. Martin and his friends are sailing in calm, foggy waters when out of nowhere, a massive iceberg shows up right in front of them. No one even had the time to react before the ship crashed; the iceberg was so huge that it mangled the boat and crushed Bladeribb to death.
Balefur's death in Outcast. He was a total jerk, but he didn't deserve such a horrible death.
There's also Swartt's horrific revenge on two dissenters. He forces one of them to feed the other a dead crow, and has to eat all of it, including the bones, which he chokes to death on. Then, Swartt has the other one executed for "murdering" the former.
Mariel's flashback sequence is scary but not particularly nightmare-inducing until the reader (possibly specifically the female reader) hits about age twelve and the Fridge Horrorimplications kick in. May or may not actually have been meant that way, but it hits the right button and aargh.
You gotta feel sorry for all the hell Abbot Durral went through in Pearls of Lutra. Getting captured by lizards, getting repeatedly threatened by Lask Frildur, and not a single beast was there to reassure him that everything might be okay (except Romsca). When shit finally hits the fan and Romsca and Lask's crews get into a huge fight, Abbot Durral is sitting in Romsca's cabin, alone and utterly defenseless. He blocks the door with a bunch of junk and simply sits in the corner of the cabin for an entire day hoping all the noise will go away. The next morning, something happens that would make any regular abbot shit himself: someone starts banging on the door and hacking away at it. Once the door has a huge hole in it, the beast on the other side shoves his head through it. Surprise! It's Lask Frildur!Cue chapter's ending.
Buppler and Braggio's deaths in The Rogue Crew. The latter is decapitated, and his head is planted on the Greenshround's foremast. The former had his spine crushed by the ship's wheel, and Razzid leaves him lying on the ground to die while he's screaming for help.
Zwilt the Shade, the Marlfoxes and Malkariss. When they first appear they are mysterious to the point of being creepy as hell. You at first know nothing about them, they are feared by basically everyone for being "Magic", "Invicible", and "Deadly". All were revealed to be frauds, but the reader doesn't know that until later on. A good example of this are the Flitchaye. In most of their appearances it was never revealed what they actually were aside from cannibalistic monsters.
Vilaya's plan in general. Kidnapping kids from all over the country even murdering one, gets even worse from there... after the kids escape they run into a hedgehog who enslaves them again this time trapping them on an island giving murderous threats and threatening to eat the younger ones if they don't be his slaves, many of these kids are just toddlers... could you imagine how traumatized they would be for life?
While the Marlfoxes are established as a pack of fratricidal backstabbers fairly early on, the last of the Marlfoxes gives himself that status by pushing his sister into a lake full of ravenous pike. Lantur was a bitch (no pun intended), but she did NOT deserve that.
Clogg's fate in Martin the Warrior, possibly. He's left all alone in Badrang's huge, deserted fortress after all the vermin who once occupied it are dead or fled. He's also left completely insane and reduced to laughing madly to himself and trying to drive off seabirds from his new domain...seabirds are carnivorous, and Clogg is stated to be fat and slow.
Tsarmina's hydrophobia episodes in Mossflower might also count. Especially at the end, when in trying to get away from the water, she somehow backs up all the way into the lake and is pulled under by her heavy clothes.
Lonna Bowstripe after Raga Bol gets killed. Picture this: you see badger consumed with Bloodwrath, and then he proceeds to use a rat's carcass as a flail to kill other vermin. And when he's done slaughtering all these beasts and smashing their bodies apart, the badger looks you dead in the eyes, and then throws Raga Bol's body against a tree. And then he smiles like absolutely nothing grotesque just happened. No wonder Toran and the other Redwallers were afraid to approach him.
Even more scary: according to the text, Lonna hunted down EVERY SINGLE VERMIN of Raga Bol's crew who managed to escape and killed them as part of his Roaring Rampage of Revenge. This implies that no matter how well those vermin hid or how far they got, Lonna tracked them and most likely killed them in a horrific manner.
In High Rhulain, Slothunog. Both in-universe and out. It's a giant prehistoric monster living in a vast, unfathomably deep lough in the middle of Green Isle. It also has a ravenous taste for flesh, and is the main way that Riggu Felis punished otters for treason.
Speaking of snakes, there is a sibling trio of snakes in Triss. As if this weren't bad enough, they are literally chained together by their tails (which are rotting from lack of circulation beneath the chain) and attack as one unit. The only way to tell they're coming is by the horrible stench that precedes them everywhere. To make matters even worse, they inhabit Brockhall, which you may remember as the place where Martin the Warrior's army stayed before Redwall was built. Brockhall is little more than an abandoned house of horrors now, and to add icing to the terror cake, the mummified remains of the three snakes' mother is in there also, forever locked with the corpse of the vermin king that killed her. Oh, and these three snakes also manage to kill Shogg, Triss's best friend.