Dudley Smith totally had it coming!
Back when Warren Ellis was writing The Authority, The Doctor (Earth’s shaman) forced the ocean to engulf an entire COUNTRY in a parallel universe that set up rape camps and committed genocide, and started to threaten the “real” world. That’s pretty cruel.
I’m not sure where’d you place the Crow, but in his movie, he kills one of his murderers in a spectacularly horrible manner.
The bad guy was a major arsonist, and the Crow took him down to the docks with his beloved car, strapped him in, and set the damned thing to explodewhen it went over the pier. So, he slowly trapped him in with duct tape, set all kinds of explosives in, and then sent him shooting off to be burned alive and/or drowned.
I’m always a little bemused by the number of people who view The Matrix as a flick to ever stop and think about…but the cheatcode-enabled lobby shooting spree setpiece is a little bothersome.
Gotta go with Jack Baur’s attack on the large fellow early in Season II. Simply to re-establish a cover with…some bad guy (memory fading), he shoots a guy, then takes off his head with a hacksaw, puts it into a bag and drives off.
Sure there was the nuclear threat, and the guy was a child molester (?) who got off, but that really punched you in the face with “Jack will do anything to get the job done”.
And this season is continuing that tradition.
It’s not really an “attack,” but some might question some of Batman’s tactics. Or at least, the effects of his tactics on the public.
I mean, look at the Joker. He always escapes from Prison or Arkham, and he always murders more people when he’s loose. It’s like letting a rabid dog run loose because you think it’d be immoral for you to to shoot an animal. 
Having just watched it for the umpteenth time this afternoon when cable was out, I must confess I’m still a little disturbed by Jim’s treatment of some of the soldiers in 28 Days Later.
Sure, they were about to do an unspeakably messed up thing, and deserved something awfully foul, but some of them couldn’t have been more than 20 and were obviously influenced by their corrupt leader telling them the future of mankind hinged on them raping this woman and little girl. And yeah, the main baddie solider deserved to die, but to have his eyes poked out while still alive and thrashing??? Yick.
Cillian Murphy is still my boyfriend, though. 
John Clark, the main character of Without Remorse, a Tom Clancy novel, dispatches a guy in a pretty nasty way.
He catches the guy who killed his girlfriend, and puts him in a depressurization chamber (like divers use). Then he starts cranking the pressure up, and dropping it down, over and over again. I think he takes pity and finally shoots him, but it’s been a while since I read the book, so not positive.
AtomicBanana—
…According to what I heard from my Dad, a long while back, Clark just dumps the guy at a hospital emergency room. But by that time, the guy has suffered such severe trauma—including enough brain damage to render him incapible of speech—that he was expected to die within a few days, no matter what they did.
Skink, a mostly good character from Carl Hiaasen’s books, is particularly nasty. In one book (I’m pretty sure it was Lucky Dog): He shoves a Club (the steering wheel lock) in a guy’s mouth, ratchets it as far open as it will go, then throws the key into the gator-infested bayou.
The Buffyverse reference in the OP made me think of Angel locking all the Wolfram & Hart lawyers in that wine cellar with Darla and Dru. That was pretty cold.
Rex O’Herlihan, the Singing Cowboy, to the Basque Sheepherder:
Okay, more of a threat than an actual attack, but still. . .
“These cuffs are made of tensiled steel. It would take you ten minutes to hack through them. If you’re quick, and if you’re lucky, you can hack through your ankle in five.”
What about Kevin Costner in The Untouchables, when he threw the guy off the roof.
That got to me, too. I hated Sisko for that. When he “died” in the last episode, I figure that he got what was coming to him.
Terminator 2 (theoretically a good guy, under John’s orders) shoots multiple cops in the kneecaps, probably permanently crippling them. He COULD have just walked up to them and knocked them out.
The two Buffy references have missed the best one IMHO:
Giles snuffing Glory’s alterego by suffocating him.
…and I wouldn’t consider him an anti-hero category, either.