Humorously subverted when Gwendolyn and her arranged fiancé Frederick meet a second time. Gwen already has a Face of a Thug that had previously made Frederick resistant to marrying her. And right before this second meeting, he thought he had just killed Gwen by accidentnote It was actually cursed princess Monika. She was wearing a dress of Gwen's that she stole, and when Frederick saw her from behind he thought it was Gwen. Also, Monika turned into a crow out of Frederick's sight after she fell off the cliff, so she didn't die either. Gwendolyn had earlier heard Syrah give a hypothetical speech for her to use with Frederick to try and reconcile with him. As she tries to remember what exactly Syrah said, she's also Trying Not to Cry because she's unused to being so confrontational; the strain of this leaves her eyes increasingly bloodshot, making it look like she has a furious, red-eyed Death Glare. Combined with her misremembering the lines in a way that sounds like she's unkillable and vengeful against Frederick, this leaves him utterly terrified.
Played straight with King Leland of the Plaid Kingdom, who has naturally red irises and is very strict with his sons to the point of occasionally being downright abusive (especially with Frederick), on top of having a rather Machiavellian approach to ruling in general.
The "tainted" or Ver'drowendar from Drowtales have red irises; they "have been seeded by a demonic entity". All drow naturally have red pupils, but this is the result of eyeshine and is an evolutionary adaptation to living underground, but results in tainted characters having red on red eyes.
And, ironically, his opposite number, Vladimir Von Helson, via heterochromias (one gray as is standard for Gaian vampires, one red apparently just for the sake of this trope).
Girl Genius: while subtle, it is seen well in this strip that Mama Gkika has red eyes. Possibly other Jägers, too.
Inverted in The Glass Scientists, as it's the calm Jekyll who has red eyes, while more dangerous Hyde's are green.
The yellow salamander/lizard-thing. It may not have been evil, per se, but it was certainly dangerous. The lizard was a house fire that killed a small child and his family.
Zimmy plays an odd variation of the trope. Normally she seems to have Black Eyes of Evil, but when she is temporarily purified from the etheric miasma that pollutes her spirit by natural rain, it turns out that her eyes are bright crimson underneath. In this condition she is a lot more coherent and amiable than her usual self, but acts as a reminder that she's not exactly normal, either way.
Hetty has red eyes and is as evil as they imply, as seen from her suggestion that Reynardine kill Antimony and her Irrational Hatred toward Adam.
The Court robots generally have green eyes, but they'll turn yellow when the robot is alarmed by something and red when they have detected certain kinds of threats. Although they're never evil, when in red-eye mode they do not respond to normal commands and will use violent force against the perceived danger without further warning.
All the vampires in Hanna Is Not a Boy's Name have red or reddish eyes, although some are more evil than others and the least evil of the four we've seen so far isn't drawn with visible irises at all.
Homestuck has Calliborn, having candy-red eyes and red swirls on his cheeks that turn into solid circles once he successfully kills Calliope. His eyes are no long red, but no less eerie, when he transforms into Lord English and his eyes turn into constantly cycling pool balls.
I'm the Grim Reaper: One of Scarlet's eyes tends to glow when she summons her scythe. Her irises are always bright red.
In Impure Blood, when annoyed. Note that her eyes can also glow blue for other magical purposes.
Kagerou: when (the aptly-named) Red takes over Kano's body, his eyes turn red. And Red is a psychopathic rapist and murderer.
Quite a few characters from L's Empire (most notably Dark Star). Pix averts this as, despite him always having red eyes due to being Dark Star's son, he's the nicest guy in existence.
In Looking for Group, most characters, regardless of whether they are evil or good, will display the "burst of anger" or bloodlust variant. Bloodrages will most prominently display it before dishing out punishment, but even Nice Guy Cale will display them in bouts of righteous anger.
Valentino, the Big Bad of Marilith, has red eyes. The effect is highlighted by the rest of the strip being mostly in black and white.
Otherworlders in Miamaska have red eyes and purple sclera. Citizens see this as a threat to their town and take action accordingly.
Noblesse: One of the major factions in the story is the nobles of Lukedonia, all of whom, including the protagonist Rai, have red eyes.
Sabine's eyes glow red in her true form. There is an early warning of her true nature in this strip, which is before she's revealed to be a fiend. Later, the glowing-red eyes are a hint for the reader that she's shapechanged.
Tycho gets these whenever he gets particularly angry or is acting particularly evil, apparently because his body harbors a dark spectre from the world of dreams.
Penny Arcade sub-comic Automata. There's something in that time signature and it changes the eyes from the standard blue to...help.
While this is not common due to the art style of Scandinavia and the World, it does occasionally show up, generally when either Åland or Finland are especially upset.
Slightly Damned: Subverted with Buwaronote At least when he isn't completelyberserk or Lakritz who are both among the kinder demons around, however red seems to be one of the most common demon eye colors and most of them play it straight. The most notable of these demons is Iratu who at first seems to be friendly but that's because he was drunk and when we see him sober we learn he is a cunning and powerful General of Hell's Army who leads an attack on a major city that kills hundreds if not thousands of innocent people.
In one story, Bun-bun the evil mini-lop rabbit is stuck with the annoying animated shadow of the groundhog who's the Anthropomorphic Personification of Groundhog's Day. Unable to attack the insubstantial creature, he's forced to suffer all its antics. But finally it manages to do something that angers Bun-bun so much that he finally snaps. He gets so angry his eyes turn red, and subsequently he emits a red aura. Insofar as there is an explanation to this, it could be that by that time Bun-bun was already a mildly supernatural being due to being saddled with being the Easter Bunny as well as the official "groundhog".
Shadow: What do you want to do? Kiki the ferret: I have a pretend karaoke machine made from a toilet-paper roll! Shadow: You like karaoke too? Kiki: I LOVE karaoke! Shadow: A one and a two and a Bun-bun: That's IT! Everybody dies!
In "Anima: Culmination", Troloria, a psionicist with godlike powers, normally has blue Glowing Eyes. Whens he gets really angry, she gets first red dots in the middle of them and then wholly red glowing eyes.
Eli of Soul to Call has red, sometimes glowing eyes. While the population at large, especially The Order believes that he is dangerous, the fact is, that he is actually very meek, and shy. The red eyes glowing means that something else has just shown up, and that is what's actually dangerous.
Dr. Schtein of String Theory (2009) has prosthetic eyes that glow a sinister red, having lost his original eyes in a lab explosion. Thus far, they seem to be foreshadowing his eventual rise to supervillainy. They even glow in the dark, much to the horror of his prison roommate.
Darko, the mercenary from The Stupiders has glowing red eyes: [1].
In Surviving Romance it's one of the signs of someone having become a zombie.
Terra has Sovereign Northazul Kalar, Evil Overlord of an empire trying to conquer the galaxy, and his son Solus Kalar, head of a Nebulous Criminal Conspiracy that started out as a private army for Northazul.
Subverted in Two Guys and Guy: Wayne thinks Guy's eyes glow red in the darkbecause she's evil. The optometrist is pretty upset Wayne didn't mention it sooner, implying it's not only unnatural but also dangerous.
Underling: Demons. This is awkward for Lazarus when he gets them, and a tail, and horns.
A variation in that Forrest constantly seems to have bloodshot eyes, meaning that it's his sclera that look red while he goes around violently beating people up.
Robin has narrow eyes with small red irises, and is a Blood Knight that thirsts to take on anyone in a brawl.
When Wolf is shown proof that Rowan was the one who took his prized bag, an aura flares about him and his eyes go bloodshot in rage. Jared compares it to a rabid dog being given meat.
Donald is one of the nastiest characters in the story, and his blood-red eyes combined with paper-white skin give him the appearance of a vampire.
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