The senators in Eureka 7. (Points for a dramatic green light in the center of the room.)
Akatsuki in Naruto were initially shown to meet in a really dark cave with only their outlines being (barely) visible.
This is eventually explainable as security protocol. When all they're doing is meeting, they pick a place nobody (including them) has ever physically gone near to minimize the chances of spies already present, and use telepresence to minimize the chance of being followed. Once their meetings start requiring physical supplies on hand, those include lights.
Before becoming the Emperor, Palpatine always appeared as Darth Sidious, hidden in shadow to conceal his identity.
Averted with the Empire. The Death Star and Star Destroyers are all pristine clean and extremely well lit.
Except for Palpatine's throne room. Clearly, he's got a taste for it.
The evil owner of the baseball team from The Natural kept his office unlit. That led to a humorous scene when the hero turned on the light on his way out, and the team owner completely overreacted. (Roger Ebert complained about the opposite device in his review, saying that Robert Redford and Glenn Close were frequently lit like angelic beings, just in case you didn't know who to root for.)
In The Truth, the evil conspiracy has their dimly lit room described so that it matches the trope well and points out a potential advantage of using it: if the room is badly lit but for one bright light, it's hard to make out anyone's face and learn his identity.
Lord Voldemort, aka the Dark Lord, is very fond of this trope. His favorite scenes for evil showdowns include an old graveyard (at midnight) and a vast chamber filled with snake statues built far underground. Also, Slytherin house, which has a far greater ratio of mean students to nice ones, has a common room that is noticeably darker compared to the common rooms of the other houses.
Lampshaded by Dumbledore, who believes Voldemort is using the darkness and the death motifs to scare his enemies. From what we heard of Slytherin, he wasn't a very pleasant person, and the students who are enrolled in his house are usually very much like him, so it's somewhat justified.
Specifically averted The Short Victorious War, in which the future Committee of Public Safety, who have not yet carried out their coup, meet in a tennis court in an abandoned high-rise—but while the windows are thoroughly blacked out, the inside is well lit.
Whether it was day or night the king could not tell. The palace of King Tarascus seemed a shadowy, nighted place, that shunned natural illumination. The spirit of darkness and shadow hovered over it, and that spirit, Conan felt, was embodied in the stranger Xaltotun.
The Druids of his own isle of Erin had strange dark rites of worship, but nothing like this. Dark trees shut in this grim scene, lit by a single torch. Through the branches moaned an eerie night-wind. Cormac was alone among men of a strange race and he had just seen the heart of a man ripped from his still pulsing body
Averted, sort of, in The Man Who Was Thursday, when the Supreme Council of Anarchy meets over breakfast in broad daylight in a very public location. Of course, as with just about any other event in the novel, there's more going on than meets the eye. For starters, none of the Council members are actually evil.
The Mediochre Q Seth Series: The Organisation Which I Represent is seen in one of their meetings at the start of The Good The Bad And The Mediochre. It's in a darkened room lit only by a single candle, which provides enough light for the various members to just about make out where they are, but prevents them from identifying each other.
Live Action TV
Star Trek: Federation starships are definitely better lit than Romulan, Borg, or Klingon ships (even after Klingons became good guys).
Stargate Verse: averted with the Goa'uld, the Ori, and the Asurans, as all of them had pretty well lit ships. Played straight with Replicators and the Wraith. Seemingly inverted in Stargate Universe, as the Destiny (and presumably the other very old Ancient ships) was darker than the hostile alien ships were so far.
iCarly: Nevel's blackmail of Carly takes place in the dark dingy alley behind her and Freddie's apartment building.
This happens in Asfour, when Itzik is taken to meet Saragousti. Justified, as Saragousti has suffered very severe brain damage several years prior, barely moves if at all, and does not speak. Kobi uses him as a dummy boss quite literally; in that scene, he keeps Saragousti seated on a revolving chair with his back to the unwitting Itzik, who is very nervous about the scene.
In The X-Files, the conspirators often meet to confer in dimly-lit, smoky rooms.
In Studio C's "Evil Asides," the creepy old lady has dark green lighting and an ominous hum whenever she makes an aside about killing the lost campers who are following her.
Towards the end of Breaking Bad, the Whites' home is commonly shown in darkness with lots of shadows, creating an uncomfortable atmosphere as Walter and Skyler descend further into the underworld. This is contrasted with the Schraders' house, which is always bright, well-lit, and roomy.
The Wyatt Family live in a dark shack in a dank swamp. When they enter the arena, the lights go out, the only light being a lantern carried by Bray Wyatt.
The Undertaker is famous for putting out the lights just by showing up. One of his trademarks is to slowly raise his arms, causing the lights to come back on.
In Halo, Covenant ships and Flood buildings are dimly lit.
Though, in the books, that's explained as the lights being in the blue/violet range, because that's the color that Elites' eyes were adapted to.
In Wario Land: Shake It, the throne room the Shake King stays in through about 90% of the game is literally completely dark. As in, the bit Wario enters from is pretty much just a black screen and the rest of it seems like only half the lights are on, to the point where you can see the villain's eyes glowing in the dark.
In the final confrontation in Brain Dead 13, where the room is entirely in darkness, and only the tiny pillars of light are seen, as well as Dr. Neurosis, Fritz, and Lance.
In Terraria when going into the corruption, the sun will become dim.
Pirate stations in Star Made are very sparsely lit with red lamps, while the standard generated stations are lit brightly lit with standard white lamps.
There's the deep dark Dungeon of Dorukan in the first mention of plot. Interestingly it doesn't seem to be that dark inside; the PCs aren't even carrying torches.
Subverted with the Monster in the Darkness, which is always shadowed by magical darkness. He is not really evil, and wants more than everything get out of the darkness. The problem is that he is the secret weapon of the villains who don't want to reveal him until the dramatically appropriate moment.
Spoofed in Exterminatus Now, when just prior to The Reveal, The Mole calls his employer, a sinister face in a green glowing darkness... who turns out the be The Mole's poker buddy who was sleeping in bed with a digital alarm clock with a green display, and The Mole appologizes for calling the wrong number. Then we get the Big Badfrom a previous arc, cheerfully answering the phone in a brightly lit kitchen, cooking dinner and wearing a "Kiss the Cult Leader" apron.
In El Goonish Shive, Lord Tedd is shown to be in a dark room in two outof three of his appearances. The third appearance is in well lit rooms. He seems far more evil in the dark room than in the well lit rooms to the point of seeming to be a different person entirely (which is not out of the question given the multiversal setting).
In The Legend of Neil, not only is Ganon's lair poorly lit, but also commonly under the effects of fog machines (fog = power), making it damn near impossible to find anything.