Parodied and lampshaded in Angel Beats!: when Yurippe laughs during the baseball tournament, she's told that she sounds like a villain.
Again in the DVD Bonus Episode "Stairway to Heaven". This time, she even mimics Lelouch and seems glad to be lampshaded.
Tension Meter 200!!!
Azumanga Daioh: While Kimura's laugh isn't a bona fide evil laugh, it sure is scary.
One thing that didn't get touched upon in the anime is that Guts of Berserk can pull off a terrifying Evil Laugh, which he did most prominently in his Black Swordsman phase when he worked in concert with the Beast of Darkness spawned from his horrific experience during the Eclipse.
Alan Gabriel from The Big O is prone to this, though it's more of the maniacal giggle type; the fact that it's Crispin Freeman of all people doing it just makes it creepier.
Creed from Black Cat has a typical villain laugh. He mostly does it when Train is involved, though.
Chapter 458 gives us an awesome one, so much the two speech balloons that contain it occupy together a good half of the page. Who provides it, you ask? Ginjo, and this time, it isn't an act.
During his fight with Rukia Kuchiki, Espada #9 Aaroniero Arruruerie repeatedly uses a vicious laugh.
Kageroza Inaba in the anime during the Gotei 13 Invading Army arc, particularly at the end of episode 333 and the beginning of episode 334.
Torpedo Girl from Bobobo-bo Bo-bobo laughs using the word "Torpedo" over and over again. It's really creepy.
Buso Renkin: Inverted by Great Warrior Chief Shosei, the Big Good of the series, who indulges in a laugh that would be better suited to a villain while giving his subordinates a comedic off-screen beating.
Accelerator gets these pretty often. In the anime they sound freakishly high pitched and mixed in with a kind of coughing noise, to further illustrate how unhinged he is. Then there's that... sound he makes when fighting Touma: KHKHKHKHKHKHKHKHKUKUKUKHIKAKAKAKAKAKAKA!!!!It's later revealed that his "laugh" is actually him speaking a very basic form of Angel.
Even though Aion from Chrono Crusade is often smooth and charismatic, in his more manic moments, he can let out an evil, crazed laugh of epic proportions. EVIL!
City Hunter: Ryo's is a rare heroic and lovable example, used whenever he is about to go on another "girls hunt."
For the protagonist of the series, Lelouch from Code Geass gets an inordinate number of evil laughs, usually when he's just pulled another utter pwnage on his enemies with some unexpected genius tactic. His most maniacal ones were in episodes 17 and 23 (quoted below) of season 1, and episodes 2, 7, and 9 of R2.
Lelouch: These hands of mine have been dirty for a long time now, Suzaku. Your coming to face me now doesn't matter at all. Hell, I welcome it even. I mean of course, you and I are friends.(starts laughing maniacally as the Tokyo Settlement collapses around him). 
His first is a sad laughter, too, after he learns that his best friend Suzaku is working for the Evil Empire that he hates to the bones.
The most maniacal ones are notable in that they start out as a low chuckle, then rise in pitch to truly deranged sounding levels.
Emperor Charles' dub laughter somehow manages to exceed Norio Wakamoto's laughter. Michael McConnohie takes it to more than just 11, he takes it to 13. AHAHAHAHAHAHA!AHAHAHAHAHA! Check it out at 8:18-8:22.
Light of Death Note indulges in an Evil Laugh when at his most sinister. In fact, in the final story, he struggles to hold in his imminent victorious laughter and ultimately fails in a scene that cranks the full-blown psycho version of the evil laugh Up to Eleven. Sanity's gone at this point. He cracks one during the infamous potato chip scene.
Say what you will about Muraki's VA in the English dub of Descendants of Darkness, he does an especially chilling, falsetto cackle which just adds to a certain mad scientist's general creepiness.
Lampshaded in an episode of Digimon Adventure 02 (dub only) when the Digimon Emperor burst into a fit of evil laughter after expounding on one of his evil plans, then stopping and muttering "Eh, it's not that funny..."
Myotismon has a pretty good evil laugh too, particularly in the first season. Used so much in the dub that the other characters comment that they're "sick of that laugh". His laugh is so awesome that the dub's editors rewound a clip of him giving a skyward cackle twice.
Even though he's an Anti-Villain, Greed of Fullmetal Alchemist has a distinctive evil laugh/chuckle, which is generally translated as something like "gwa-ha-ha-ha-ha". On a couple of occasions in which he's Laughing Mad, it can be kind of disturbing. The psychopathic Envy provides a straighter Evil Laugh on ocassion. Also, while generally a collected Affably Evil, early on, when he sees explosions and chaos going on, Mad Bomber Kimblee starts laughing insanely. Finally, toward the end of the series, Father does a really disturbing Evil Laugh while carrying out his master plan, which is particularly scary because he has Voice of the Legion at the time.
Full Metal Panic!!: A teenage terrorist in his enormous Humongous Mecha unleashes a hysterical yet pretty normal laughter while devastating a city. However, megaphones in his mecha repeats his laugh all over the city, so it sounded sufficiently evil.
Fushigi Yuugi'sTomo, surprisingly, does this more often than Nakago, who can't even match up to the former's signature laugh ("Kakakakakakaka!"). Mayo Sakaki, for a bratty 16-year-old, has an evil laugh creepier than Nakago's.
Yuno Gasai from Future Diary erupts into this big timeafter she manipulates Yuki into killing Hinata. Just another reason why she's the prime example of a Yandere.
Heero Yuy from Mobile Suit Gundam Wing does this in the first episode but drops it after that. Chief Engineer Tubarov does it too, just before his death.
Speaking of Gundam, Cima Garahau from Mobile Suit Gundam 0083: Stardust Memory does this when she's beginning to realize the true objective of Operation Stardust, a Colony Drop. Ironically, it's either faked or a brief moment of Laughing Mad; Cima is not on board with this plan. At all.
Haruhi Suzumiya does this at least twice in the light novels, both after her HeelFace Turn. The first is in "Snowy Mountain Syndrome", and the second is in "The Melancholy of Mikuru Asahina".
Katsuhiko Jinnai from El-Hazard: The Magnificent World (particularly the OVAs). In the original Japanese, he simply sounds like a megalomaniacal Evil Overlord [tm] when he laughs. In the dub, he sounds completely unhinged. It's both hysterically funny and extremely creepy at the same time.
Katekyō Hitman Reborn! features two characters that fit the trope: Belphegor's "Ushishishi!" and Mukuro's "Ku fu fu~" — the latter character actually managed to score an Image Song titled "Kufufu no Fu". Both character's image songs feature solos of them doing their laughs.
Xanxus also had one, although it's less unique and well known compared to the other two previously mentioned. He tends to have it whenever he goes off ranting about how everyone else is trash.
Even Byakuran got one during his fight against Tsuna. He sounds like a clown.
Supervillains (Heel wrestlers) in Kinnikuman tend to have very distinctive laughs. There are many examples, but some of the best examples are those of Ditto Fighter Stecase King ("Kekekekekeke!") and Joke Character villain Kinkotsuman ("Muhyohyohyooo!")
Ashuraman's laugh ("Kakakakakaka!") is so distinctive, it's actually used as a lyric in his theme song.
King Dedede and Escargo(o)n from Kirby: Right Back at Ya! let out an evil laugh all the time, even when they're just laughing about something innocent. They provide the image.
Lord Dearche of the Materials lets off some pretty impressive cackling when announcing her presence.
Friday Monday from Madlax is of the third category, perhaps even the epitome of the third category, as he sometimes struggles to contain his evil laughter in times of victory and will cackle for quite some time.
Despite being called the "The Uchihahaha", Itachi's Motive Rant did not actually involve laughing (though it sort of looked like he did), just overacting. An event which truly lives up to that name comes nearly a hundred chapters later, but uttered by Sasuke. Not simply because he was feeling evil, but to mock Kakashi when he tells Sasuke to stop being so obsessed with revenge.
King Hamdo: *laughing maniacally* I have to laugh at them! Look at those losers on all fours! I'm gonna laugh and laugh until I can't laugh anymore. *calmly* What then? Very simple. I'm going to shoot them dead.
One Piece not only has several characters performing the Evil Laugh, but usually, every character who performs the laugh has a unique and distinct version of it that only that character says. For example, Marshall D. Teach aka Blackbeard's signature laugh has a "Ze" sound to it, and Sir Crocodile's laugh is dry and monotone.
In Pokémon Generations, they managed to make a giggle sound incredibly creepy with Courtney of Team Magma in Episode 7.
In Princess Tutu, Drosselmeyer is very fond of his evil laugh. He's an old, insane character, which makes him a pretty good example of the evil wizard type. Mytho also starts letting out evil cackles in the second season after their FaceHeel Turn.
Also parodied in one of the specials. Yukimura gets the idea that his team has to have more fun while playing. Sanada and the aforementioned Kirihara promptly try to please, revealing that those two just CAN'Tlaugh normally. Poor Yukimura has no choice but to give up.
Prince Sharkin in Raideen had an evil laugh that was extraordinary in its legnth, volume, resonance, and the sheer amount of scorn it conveyed. It was so epic that his voice actor got typecast as villains for the next decade.
Ronin Warriors: EVERY VILLAIN gets his shot at an evil cackle—usually multiple times in one episode.
Rosario + Vampire: Inner Moka, while not evil, has a couple instances of this in Season II: in chapter 1, after dishing Tsukune punishment for touching her and telling him he has a slim chance of seducing her ("Want to know your odds?"), and again at the end of chapter 6, right before curb-stomping the doppelganger that dared mimic her body and abilities.
Rozen Maiden: While definitely far more mischievous than evil, Suiseiseki manages to pull this one off pretty well when playing pranks on the other characters, and once when playing the evil queen from Snow White in a rehearsal for a school play, she does it in an extremely convincing manner.
And then in Träumend, when Jun becomes her medium, she gets a power boost and laughs like crazy while fighting Barasuishou and saving the others.
Yamori is clearly having the time of his life whilst torturing Ken Kaneki, bursting with maniacal laughter as he breaks the boy further.
After being captured and experimented on by Aogiri Tree, the formerly good-hearted investigator Seidou Takizawa becomes a chortling maniac, letting out gleeful laughter whenever being launched into battle.
The Clowns are masters of this. Roma's laughter ranges from girlish giggles to shrill cackles. During his fight with Renji, Uta, for the first time in the series, lets out a wild batch of mocking laughter at his friend.
Niwe, The Caligula from Utawarerumono, is known by fans for his intensely annoying "GYAH KA KA KA KA KAT" laugh. He would occasionally use it more than once per episode. Apparently, he was known for it by characters too, since just when Hakuoro thought they were rid of Niwe, his laugh returns with a vengeance in his dreams.
The Vampire Princess MiyuOAV. Miyu is sometimes heard laughing in the end of each OAV and it's a soft, child-like, almost gentle laugh. However, due to the circumstances and Miyu's own nature, such giggles potentially can be more horrifying than a typical Evil Laugh.
Dr. Faker has a fair bit in ZEXAL though it's probably fake, ironically, and Tron combines this with Creepy Child magnificently. But not even the incredibly sinister chuckles of Don Thousand can compete with Laughing Mad Vector, for whom it's normal to have half of his dialogue as Evil Laughter. It's usually not a good sign.
Most villains in Yu-Gi-Oh! tend to have an evil laugh, but Yami Bakura's stands out the most. He starts constantly laughing at the start of the Battle City Finals, and those laughs get more nightmarish in the Millennium World Arc. Bonus points for being voiced by Rica Matsumoto.
An anti-heroic example is Seto Kaiba. After his victory against Zigfried, he starts laughing like a villain. It's Kaiba after all.
Jaeger of Yu-Gi-Oh! 5D's has a subdued yet equally sinister laugh of "Hi hi hi!". The dub version, Lazar, does not.
Professor Cobra in Yu-Gi-Oh! GX, as well as the appropriately named Brron, Mad King of Dark World.
Saiou/The Light, has the creepy high pitched kind that illustrates his insanity excellently.
Yusuke has some fun with this one in Yu Yu Hakusho. After dying a second time and reincarnating as a half-demon, he does this along with a little speech to toy with the elite squad of soldiers dispatched to destroy his corpse and prevent said reincarnation. They fall for it, if only because it's what they expected to happen anyway, and he has a good normal laugh at their expense immediately afterward.
Elder Toguro also has a creepier version of this trope played straight.
Hiei lets out a good one while Botan risks her life trying to keep Kayko from turning into a demon. It backfires as it helps to piss Yusuke off.