The Solars in Exalted are the divinely empowered "chosen ones" of the Sun itself, with light motifs and abilities, who were overthrown and murdered long ago for being mad, inhumanly monstrous tyrants.
Their Patron, the Unconquered Sun, is a pretty good guy, however he's solidly addicted to the games, and his constant insane virtue means he nearly constantly has to be suppressing some aspect of his being to be able to function at all.
Also: if said light is green, it's time to leave very abruptly, because you are now dealing with the demons of Malfeas. And if the source of said green light is on the ground and near you, you are dealing with Ligier or Infernal Exalted. In either case, you're probably screwed very thoroughly.
Then we have the C'tan who are even more evil than the Chaos gods and who are trying to kill everything in the galaxy. They are called Star Gods because they originally lived on stars, it is also implied that they are actually the souls of the first stars. The weapon used by the leaders of their mooks is even called a Staff of Light.
Then there's the Ethereal Tau caste who are (probably) brainwashing the other Tau into doing their bidding.
Both the fantasy and sci-fi versions of Warhammer share the Chaos God Tzeentch. God of Change, born from the embodied hope of all sentient beings, patron of progress, evolution and elevation. This ultimately leads to him manipulating any and all creatures in the cosmos, encouraging backstabbing treachery and endless anarchy, and transforming anything that catches his attention into a nightmarish mass of Body Horror.
The faction of Imperators (gods) and Powers (Player-character demigods) in Nobilis called simply 'The Light' exemplify this. While they believe above all else in the survival of the human race, they are not picky about the means. They will preserve humans and their well-being wherever possible, but if they have to kill or ruin the lives of a hundred people, or a thousand, or a million, to perpetuate the existence of the race, they will do so without hesitation.
To put things in perspective, the Light was responsible for both breeding the divinity out of mankind in exchange for a larger population and then later for causing the Biblical flood to save the surviving humans from the Dark's plan to cause humanity to wipe itself out with overpopulation and arms races.
Similarly, Angels and others that follow the Code of Heaven are more concerned with Beauty than with mortal concepts of goodness. The closest they get is considering Justice to be a form of Beauty. It's also their will that closes the doors of Heaven to mortals to preserve its beauty, condemning nearly all living things to a cycle of endless reincarnation until damnation.
Ananda is a being of indescribable beauty. He is probably one of the closest things to a good guy in the Council of Four that rules Earth, and his realm of Cityback shores up the progress of all cities. However, he's also the Imperator of Murder (meaning that all murders derive from his existence), his beauty kills or drives mad all who see it, and a prophecy prevents him from taking action against the openly evil (and yet loyal to Creation) head of the Council of Four, Lord Entropy.
The antagonists of this setting, the Excrucians, sort of follow this trope as well. They are the most beautiful beings in the settings (more so than even the Angels), but their goal is the destruction (or possibly theft) of all of Creation, both good and bad.
Lastly, there's Lucifer, whose angelic glory is utterly uncorrupted by his time in Hell, but who is still pledged to lead the cause of Hell and damnation for reasons of personal conviction.
The Eladrin, a branch of outsiders in 3E and elves in Fourth Edition who live in big shiny crystal cities in the beautiful Feywild, are inhumanly beautiful and custodians of ecology... And are noted as being rather frightening due to their alien nature and, as all PC races are in 4e, listed as "any alignment". So while an eladrin can be goody-two-shoes Purity Sue, he can be a real prick as well.
Third Edition had beings from the Positive Energy Plane who loved nothing more than combat, to the point where they would take vacations to the Material Plane, offering to bond themselves to warriors who would get some pretty significant powers in exchange. In fact, the fast healing that they provide was so powerful that if you weren't actively being injured, your body would explode from the buildup of positive energy. The kicker? They risked dying themselves if they stayed in the Material Plane for more than a week or two.
The Positive Energy Plane itself practically embodies this trope; it's a world empty of matter but filled with brilliant healing light, which restores living beings to full health — and keeps pouring energy into them until they explode. By contrast, the Negative Energy Plane is no more harmful than the Elemental Plane of Fire, it hurts things not immune/sufficiently resistant to fire/negative energy, but is harmless to anyone who is, and the plane has residents that can exist on the prime material unharmed. That said, the Plane of Positive Energy has one advantage for ordinary mortals: the explosion thing can be perpetually kept at bay with perfectly nonmagical meansnote have a knife. Cut yourself every now and then.
While not Good, the Positive and Negative Energy Planes really aren't Evil either. Like all the Inner Planes, they represent forces of nature at their most extreme. Dangerous, yes, but no more evil than a hurricane or a tsunami is.
The 3E/3.5 spell Searing Light can be used by casters of any alignment. It involves shooting someone with a light beam.
In 4E, the warlock class can make a deal with beings who reside "behind the stars" to use their powers. Quite a few of their attacks do radiant (light) damage— though given the nature of the beings, it's more Light Is Beyond Good And Evil. And some stars are very evil, somewhat among the lines of Eldritch Abominations, given the nature of their most powerful servants, the starspawn, mentioned in the Monster Manual guidebooks.
Also in 4E, the paladin class is no longer limited to being Lawful Good. Rather, they are now a class of holy warriors dedicated to a god. Many of their attacks do radiant damage regardless of their deity's nature. In fact, the player's handbook acknowledges how disturbing it would be for players to fight a champion of evil whose weapons explode with holy light.
Radiant Energy in general counts. Vaguely equating to Positive Energy (pure life force) in the older edition, Radiant energy is described as "pure light" and is most commonly found in the Divine classes (arcane, primal and psionic classes also get a sprinkling of Radiance powers). It's a damage keyword — meaning that it's specific use is, generally, the same as a Fireball or Acid Storm.
Specifically, Radiant effects usually are caused by divine powers, rather than "laser magic". Considering that there are just as many gods and goddesses of darkness, evil, chaos, shadow and hatred as there are those of light, good, order, charity and love, it kind of makes sense.
Angels themselves in 4e; beings of pure light/energy, they're not necessarily good or evil; simply, they serve gods. Some serve good gods, others evil ones.
The Quasielemental Plane of Radiance in Planescape cosmology does it literally. No, it's one of most beautiful places in The Multiverse (some Celestials travel just to look at it) and hostile beings are very rare there — even mephits are quite harmless. The problem is, the whole plane is bright — like a sun disc, but from every direction at once. The problem is, it causes a few inconveniences to most non-natives: the light is near-instantly blinding, the air is absent, and everything unprotected suffers more than half of heat damage it would take on the plane of Fire. It's that bright. It's placed between the planes of Fire and Positive Energy ("life").
The Dungeons & Dragons world Eberron has no restrictions on what alignment a cleric of any faith has. This means that the Church of the Silver Flame, a lawfully good religion centred around a divine silver-coloured flame created/tapped into by the sacrifice of most Couatl (beings of good) and The Messiah of the Church has its share of Knight Templar and self-serving hypocrites (they also have corrupted secret followers of the Shadow in the Flame, but that is another trope). The same applies to any good faith, although most aren't quite so associated with light.
The Forgotten Realms had the old incarnation of the god Amaunator, a god of the sun... and of order, law and bureaucracy, with all that entails for clerics taking 'order'too far. He wasn't evil, but neither was he good. His current incarnation is good, however (it is complicated, but boils down to being sort-of dead but not quite gone, and then fully coming back via another aspect that was good).
In Pathfinder there are the Shining Children- weird alien things, Lurkers in the light- VERY evil fey who have light based powers and will mess your day up, and Aeons- not quite "light based" but some appear to be made of cosmic energy and light. But they aren't good... or bad. They're very neutral.
In Magic: The Gathering, white's worst traits are being dogmatic and authoritarian, to the point of ruthlessness and xenophobia.
Mark Rosewater writes an extensive article here discussing the color's motivations. His style summary may not reflect recent sets since it was written in 2003.
The daimyo Konda from the Kamigawa block, being not only white and villainous, but also opposite to Toshiro Umezawa, which is heroic. Konda stole a "god" to gain immortality, and while justified as to keep his people happy it comes across as rather selfish, unusual for a person aligned with white.
Lieutenant Kirtar, listed in Feathered Fiend, is also a White aligned villain that is essentially a proud, arrogant Jerk Ass.
One of the Archenemy decks is based around the colors green and white, which are usually associated with life and nature. Its theme? "Trample Civilization Underfoot".
The Scars of Mirrodin set introduced white Phyrexians in the two last extensions (Phyrexians being the big baddies of Magic)... Though, given their general appearance, it crosses the line between Light is not Good and Obviously Evil.
Depending on how you interpret the unusual listing of the New Phyrexian factions (WBUGR instead of the usual WUBRG), it can also mean that White is now the most phyrexian colour.
It also includes a white spell called "Wrath of God." Its effect? Destroy all creatures. A double-edged sword if your creatures aren't indestructible.
The "Wrath of God" card used to be this trope's page image. Also, the card later got a Dark Is Evil counterpart named "Damnation" that does exactly the same thing.
All colors have some Cards of Mass Destruction, but only white has mass destruction to ALL kinds of permanents, except Planeswalkers (Wrath of God for creatures, Armageddon for lands, Akroma's Vengeance for artifacts, creatures AND enchantments...). White also has Elspeth Tirel, a Planeswalker that can wipe everything but lands and tokens. Curiously, however, the color that has the most "efficient" board wipe is blue, in form of Upheaval
"Those who fear the darkness have never seen what the light can do."
The Selesnya and Azorius guilds from Ravnica. The first, aligned with White and Green mana (both the stereotypically "good" colours), are brainwashing cultists who ever now and then attempt a Gaia's Vengeance and who are extremely hypocrital and violent, while the latter are White and Blue power hungry politicians obsessed with laws that prevent the status quo from happening. The Orzhov also qualify, but the first, being also aligned with Black mana, combines both Light Is Not GoodwithDark Is Evil. The Boros, aligned with White and Red mana, tend to be opressive, belligerent and very violent, and their current leader, Aurelia, is a bitch who usurped the throne of the previous leader because she was an outcast, but it's unknown if they have reformed for the better or not.
According to Mark Rosewater and Serra (as well as some of his guises and spells), Urza is White/Blue. He also caused countless cataclysms, devised an eugenics program (and was a general social darwinist), manipulated his own allies against themselves and ultimately joined Phyrexia.
The Eldrazi are always depicted with bright colors and in the light of day. That just makes it easier to see the destruction they spread with their mere presence.
Scion gives us Akhenaten, the Titan of Light. How is light bad? It burns away everything it focused on, leaving nothing but empty, unending light. Akhenaten's avatar (i.e. its brain), Aten, desires nothing more than the worship of every living thing. He's quite good at turning his enemies Brainwashed and Crazy... and then making them into suicide bombs.
On a lesser level, Kane Taoka, the leader of the sample evil Scions. He's a son of Amaterasu, the Shinto sun goddess. Although he does eventually become the god of darkness.
In Yu-Gi-Oh!, the Light Attribute is usually associated with goodness and purity, but not always. Some well-known Light monsters are Obviously Evil. Well known examples include the Ritual Monsters Ruin, Queen of Oblivian and Reshef the Dark Being, the whole Fabled archetype (who are Fiends that look much like Fallen Angels along with a few mythical Beasts thrown in) the hideous aliens of the Worm archetype, and the Arcana Force archetype, which seems based on Cthulhu Mythos.
In Paranoia, white is reserved for High Programmers, who have huge amounts of power and trust with which to screw you over (including reprogramming The Computer) and are not shy about doing so.
In Nomine is built around playing with this trope (and similar ones). While the angels are ostensibly the good guys and the demons are the bad guys, the angels are decidedly not nice (except for the ones who are exceedingly so), and often don't have mankind's best interests at heart. The game also lets you play the demons' side of things; and one style of play (known as "playing In Nomine backwards") portrays Heaven as a bunch of jack-booted control-freak thugs who wish to suppress and dominate everyone.
In Battletech, the Word of Blake uses a lot of motifs evocative of angels. They are, however, probably the only group that outdid the Usurper, Stefan Amaris himself, in quantity of atrocities during the Jihad. They earned the irredeemable enmity of the entire Inner Sphere, Successor States and Invader Clans alike, and were completely stomped out of existence to make them stop their atrocity spree.
Dungeons & Dragons and Fighting Fantasy both feature evil will o' the wisps as monsters. Appearing as floating orbs of light, they try to lure other creatures to their deaths in swamps and forests. If they get impatient, the wisps may simply decide to kill their prey themselves with bolts of energy.