The main villain of My Little Pony: Equestria Girls is Sunset Shimmer, who is bright yellow/red and has a sun for a cutie mark, and has a teal aura. Even her demon form is brightly coloured and uses light/fire balls.
Dr. Light, who even makes a joke about it while fighting Raven, the Teen Titans' version of Dark Is Not Evil. After pasting her with a laser bolt, he asks her, "What, scared of the light?" (Then her Superpowered Evil Side got him, right after mockingly asking him if he was afraid of the dark. He wound up being so for a while. In a later appearance he fought as usual against the Titans until seeing Raven, at which point he instantly surrendered.)
Brother Blood wears white and yellow and is quite charismatic. His powers are psychic in nature, but otherwise seems light aligned. Bonus points for Word of God, which states that he was intended to be a foil of Slade; while he hides in the shadows, Brother Blood likes being the center in the spotlight.
In the Christmas episode, Stan helps cute forest critters build a manger for their baby to be born in, only to find out they're satanists and the baby is the Antichrist. They are so dark and twisted, they joyfully sacrifice one of their own to the devil. In fact, their nemesis was a scary-looking mountain lion, whose job it is to prevent the birth of the Antichrist.
The furry little animals later return in Imaginationland as part of the Evil Imagination army. They prove to be the most evil of the group, as all of their actions involve violent rape, urophilia, or some other horrible thing that squicks out all other evil creatures. The fact that they're borne from Cartman's imagination might come as no surprise.
The Knights of Standards and Practises from "It Hits the Fan" are Knight Templar in nature, although they were clearly the lesser evil. The forces of Heaven, while technically good, sometimes get less pleasant.
Interestingly, Jackie Chan Adventures presents dark (well, "yin") as good, and light as evil. Well, more like nice and jerkass than good and evil. This is in keeping with Chinese symbolism, in which Yin represents coolness, shade and calm, while Yang represents heat, fire (or sunburn) and passion, and neither is entirely good nor entirely evil.
In "Chaotic Crisis", Maxor, during an attempt to force the Underworlders back to Perim, reveals his intentions to conquer Earth for the Overworlders ( It was All Just a Dream).
Daemon, the most powerful villain in ReBoot, is brightly colored, speaks with a soft French accent, and is generally styled after Joan of Arc. She also wants to unite the entire Net under her order and then destroy it, to create perfect order in oblivion. The methods of her followers are an obvious reference to religious fanatacism, complete with digital gospel singers and all.
In a segment of The Simpsons "Treehouse of Horror VI", Homer gets trapped in a 3D dimension. When Reverend Lovejoy asks if he sees a light Homer says yes and the Reverend instructs him to "Head into the light my son." Cue the sound of electricity and Homer screaming in pain.
In a ThunderCats (1985) episode, the titular feline heroes are faced with two aliens: one is a gruff, armored reptilian(?) and the other is a gentle-voiced, delicate golden robot in white robes. The golden robot claims he's being hunted by the reptile (either they're at war or it's a cop chasing a criminal); naturally the opposite is true.
Although good, the Air Tribe from Gormiti: The Lords of Nature Return resort to anything to defend their people, fitting well on the Knight Templar aspect of this trope; this is exploited by the Fire Tribe, which convinces them to do a Heel–Face Turn on the backstory of the series, with not very pleasant results. Being modelled after fairies and angels, and with white, yellow/gold and bright blue as their main colouration pattern, they look rather pleasant compared to the other tribes, which have quite grotesque members. An actual Light tribe exists in the franchise; they just haven't showed up in the series. Since the show is quite Animesque, it wouldn't be surprising if they were Knight Templar-ish as well...
In Cats Don't Dance, Darla Dimple looks like a sweet, cute little girl that wears pink and or other light coloured clothes, she is blonde and has blue eyes, and she even goes as far as playing the role of an angel in a movie. Sure she must be innocent and sweet, right? WRONG!!!!
Jiminy Lummox, Stimpy's conscience in The Ren & Stimpy Show. A Jiminy Cricket expy who appears in a burst of light and goody goody sounding music, offering platitudes with a twisted attempt at a warm facial expression and demeanor. He's really a dense, dangerous, domineering jerkwad who himself abuses Ren against his own conscience when he sees Ren pick on Stimpy (even when Stimpy deserves it, like using Ren's teeth to descale fish), and leaves Ren entirely alone otherwise despite having been lent to him to be his temporary conscience (since Ren ordinarily has none).
On Young Justice, the Big Bads (so far, at least) are a council referring to itself as the Light. Initially its leaders are not seen directly except as bright silhouettes on computer screens. It should be noted that the Light don't see themselves as being Evil, but rather uplifting humanity to a place of dominance in the galactic community. What makes them Evil is pretty much what they do to reach their goals.
Little Suzy, the usually pretty blonde little girl often spouting cute nonsensical words and adorable in almost everyone's eyes on Phineas and Ferb ...is actually a monster. She makes Candace's life a living hell whenever she's around to the point of Candace becoming frightened of her. This also applies to Buford. "Justified" in one episode where she tells Candace that it's just how she acts in order to control her older brother... which doesn't make it any better.
The Big Bad in Batman Beyond's first season, Blight, emits a bright radioactive green glow. This contrasts with Batman, who is dark, and can even turn invisible.
Amon from The Legend of Korra. He wears a white mask with gold patterns and a sun symbol, has a Knight Templar goal, and uses a special brand of bloodbending to mimic the Avatar's energybending, making him a false prophet.
Unalaq from the same series, who follows the Knight Templar mold and uses a waterbending method that infuses water with golden light and purifies evil spirits. He's an obnoxiously self righteous jerk and invades the Southern Water Tribe. Though he can also infuse waterbending with dark energy, making him an example of Dark Is Evil as well.
Ultimately, while Raava herself is good, the fact that people like Unalaq can use her essence willy nilly showcases that light is neutral in this setting.
Several of the spirits that Jinora and Korra meet in the spiritual world, which work for Unalaq but can pass off as normal light spirits. The "best" example is probably the dragonfly-bunny spirit.
Miss Power from WordGirl looks like a superhero but anything but heroic about her...
Played with in the Mortis arc in Star Wars: The Clone Wars: The Daughter is the embodiment of the Light Side, and while she herself is good, The Father implies that too much of the Light Side would destroy the fabric of the universe, meaning even the Light Side isn't an entirely good thing.
The Daughter was also perfectly willing to kill Obi-Wan on the orders of the Father.
Anarky, the Big Bad of Beware the Batman, is dressed in an all-white, shiny costume, sharply contrasting with Batman's all-black one.
Detroit Deluxe from Motorcity is clean, sun always shining, and is represented by the color white. It is also an oppressive dystopia that denies basic rights.
Angelica Pickles from Rugrats. When she's around adults she's a sweet, adorable polite, little angel that melts the hearts of all the adults but when she's alone with the babies she's a hateful, agressive little brat who enjoys torturing the babies and taking their stuff. Although she always gets in trouble in the end.
Yellow Diamond from Steven Universe is named after a gemstone associated with sunlight in gemstone mythology and is represented by the color yellow. Doesn't stop her from being a callous Galactic Conqueror who wants nothing more then the destruction of Earth and everyone on it.
Blue Diamond has been repeatedly been compared to having a saint like appearance along with Garnet's portrayal of her as calm and light spoken but is just horrible as Yellow Diamond by trying to murder the Pre-Crystal Gem Ruby for altering Sapphire's vision of Homeworld winning the war and fusing with Sapphire by accident. This is made worse by the fact Ruby wasn't aware of Sapphire's vision and was performing her duty of protecting Sapphire per her duties as her guard.
Rick and Morty once met a small nebulous being that looks like a gas cloud surrounded by cell nuclei. Rick warns Morty not to free him from the prison that they find him in, but of course Morty doesn't listen because it seems like Rick is just being his usual selfish self. Just before entering the portal to his own dimension, the nebulous being gratefully tells Morty that him and his kind are coming to eradicate all organic life in the universe which they see as a disease, almost seeming to think that Morty would look forward to this as much as he does. Then Morty kills the being with a laser gun while crying.