There's something about the name "Khan" that just sounds threatening and powerful to people in Western countries. So it follows that in works of fiction, if you want a really good evil name for your villain, and Kain is out of the question, "Khan" will do just fine. "Kahn" and other alternate spellings are also available.
The reasons for this may stem from Turko-Mongol cultures, for whom the word 'Khaan' (pronounced 'haan') was the equivalent term for a king or lord. Genghis Khan is the one most folks have heard of, but other languages and cultures used "khan" as well. Thus, the name "Khan" for a villain in a work of fiction implies a powerful, dangerous ruler of a people or nation, and possibly one with a historical basis or a cultural heritage behind them. It may also just be for the Rule of Cool: "Khan" gives you Xtreme Kool Letterz, after all.
This doesn't of course apply to other parts of the world, such as nations like Afghanistan, Pakistan, India where the surname has a lot of positive and heroic connotations, with a number of famous kings, sportsmen, and movie-stars having this as their surname, and it being seen as a very noble, and bold name.
An example of Names to Run Away from Really Fast.
- The DC Universe supervillain Manga Khan is an intergalactic trader with a gaseous body who wears a metal suit to give him his form. The suit makes him immune to harm as well as granting him tremendous strength.
- Yuga Khan, the father of Darkseid and the only being in creation considered more evil than he is. However, he's only concerned with the Source itself rather than universal domination.
- Shakara: One of the alien emperors that Shakara has set his sights on is a violent Blood Knight named Warlord Skulka, Supreme Khan of the Xorn Empire.
- X-Treme X-Men had Khan was a tyrannical dictator of a vast extra-dimensional empire who once sought to take over Earth and add Storm to his Battle Harem, by force.
- Ms. Marvel (2014) aka Kamala Khan thoroughly averts this of course, being that she's a superhero born to immigrants from Pakistan where there is no stigma attached to that name at all.
- The leaders of the Mongol and Timurid invasions in A Scotsman in Egypt are khans, though in both cases they're mere figureheads having obtained their position through connections, the truly dangerous ones are their seconds-in-command.
- The Big Bad in James Bond film Octopussy is the Wicked Cultured Kamal Khan.
- Khan Noonien Singh is the Big Bad of Star Trek II: The Wrath of Khan and Star Trek Into Darkness.
- The Big Bad of The Shadow is an Asian psychic named Shiwan Khan. Justified in that he claims to be the last descendant of Genghis Khan. Which is unlikely: not only can approximately 1 in 200 men in the WORLD make that claim, but "Genghis Khan" was just a regnal name (literally meaning "universal war-leader") and his real name was Temujin Borjigin.
- The Jungle Book has Shere Khan the tiger, hunter of man and ruler of the jungle. The Disney film and its subsequent sequels and adaptations make him into a full Big Bad.
- Pseudo-example in A Song of Ice and Fire. The dothraki are based on many nomadic peoples, but the Mongol and Hun influences are particularly strong; so it is their leaders take the title "khal," and many other words in their language derived from the same.
- The Star Wars Expanded Universe/Legends has both the Sith Lord Skere Kaan, and the Yuuzhan Vong commander Loiric Kaan.
- The iconic Khan Noonien Singh of Star Trek: The Original Series is an Evil Overlord from Earth's distant history, put in suspended animation and revived during the series to become one of Captain Kirk's greatest enemies. He's said to be an ethnic Sikh (though played by a Latino, Ricardo Montalban).
- Xena: Warrior Princess: the Story Arc set in China features an enemy warlord named Khan, based on Genghis Khan.
- Doctor Who:
- One of the Daleks from the Cult of Skaro is named Dalek Caan, pronounced the same way as Khan. Although the "villain" part of the trope was actually subverted in the third story arc he appeared in, where going somewhat mad caused him to switch sides and betray his fellow Daleks.
- Inverted with Thirteenth Doctor companion Yasmin Khan.
- Two episodes of NCIS involve our heroes dealing with a cyberterrorist named Ajay Khan. In both cases, however, they're using him to catch even worse bad guys.
- The toku series Denkou Choujin Gridman has a computer demon named Kahn Digifer. Its American adaptation Superhuman Samurai Syber-Squad, where the same character (now an unfriendly artificial intelligence) is named Kilokahn, also counts.
- First played straight, then averted in Funky Winkerbean. Funky's helicopter is shot down by the Taliban and he's taken prisoner by a group of Afghan bandits led by a man named Khan. He eventually escapes and is pursued by them. When he returns to Afghanistan as a civilian contractor to work on clearing minefields, Khan has started working for the same organization as a local guide, and saves Funky's life when he steps on a Bouncing Betty.
- Warhammer 40,000 actually averts this with the White Scars chapter of Space Marines (Mongols IN SPACE! having traded their horses for huge weaponized motorbikes), who have always been loyal to the Imperium and use Khan as an indication of leadership (their Primarch was Jaghatai Khan, their rank for Chapter Master is Great Khan, etc.).
- Played straight: where the Fantasy Counterpart Culture to the Mongols are the Always Chaotic Evil ogres and hobgoblins, with the hobgoblin's leaders known as Khans.
- Also with the Kurgan, who are a much better researched Fantasy Counterpart Culture to the Mongols and Steppe Warrior cultures in general and in the service of the Chaos Gods too boot.
- A particularly old and repulsive Chaos champion was the Kurgan Maggotlord named Tamurkhan, who could possess the people who killed him and retain their abilities for a while until their bodies rotted away. He also gets away with a double for Names to Run Away from Really Fast since he derives from another great Central Asian warlord in addition to Genghis Khan, Timur, his Spiritual Successor who nearly reunified his empire.
- One of the sample antagonists in Spirit of the Century is the evil conqueror Gorilla Khan, an uplifted gorilla— although his cape and helmet make him look more Roman than Mongol.
- In BattleTech the leaders of the Clans are known as Khans, the second -in-command of a Clan is known as saKhan and the leader of all the Clans (when such a thing is necessary) is the ilKhan or "Khan of Khans".
- Obscure collectible battle game Fistful of Aliens has Jangutz Khan, the "vicious and cruel" ultra-rare figure. While none of the characters in the line were truly "good," Jangutz was insane and powerful, and enslaved other races.
- In Mortal Kombat, "Kahnum" (note the spelling difference) is apparently the title of the Ruler of Outworld, and the current ruler upon being elected is given a new name that includes the word "Kahn." For much of the series the Big Bad is Shao Kahn The Konqueror, a violent, barbarian warlord. His successor in Mortal Kombat X is Kotal Kahn (formerly just called Ko'atal) and is actaully a subversion to this Trope. Despite the title and position as Emperor of a violent war-filled realm, Kotal is a Noble Demon who, at his worst, is just an Anti-Villain. Averted with Past!Kitana in ''Mortal Kombat 11, with the former have killed Shao Kahn of the past after Kotal's Career-Ending Injury decide to pass the throne to her.
- Fallout has the Khans as a gang of raiders, later reformed into the Great Khans. The latter particularly take inspiration from Mongolian history, and a possible ending for them in Fallout: New Vegas has them emulate the Mongolians further as a basis to reform their tribe around. Their leader is also named Papa Khan for further alliterative appeal.
- Three examples from that series exist. There was the original group of Vault-exiled raiders called the Khans, their successors - refounded after the first group's extinction - called the New Khans, and finally the Great Khans, which reformed from the scattered New Khans and took over a big piece of Nevada, before being whittled down to Red Rock Canyon. If the Courier convinces them to do so, the Great Khans will just leave Nevada to the NCR and go conquer Wyoming and with the help of the Followers of the Apocalypse create a mighty empire. Or you could convince them to join Caesar's Legion and have all of their tribe history to be stamped out and forced to become a gear in the Legion war machine.
- In Crusader Kings the Altaic (steppe) cultures all use "khan" where Europeans use "king", so given the game's Video Game Cruelty Potential and realpolitik this is true more often than not. The games also feature event invasions by the Mongol hordes, up to and including Temujin, Genghis Khan, himself. (A Mongol Player Character can even declare themselves Genghis Khan in the second game.)
- Khan is the villain's name in Broken Sword. He is a Professional Killer from Syria and member of an assassination cult called the Hashashin.
- Magicka has an Orc warlord named Khan appearing along with a large invading army. While Khan may be a semi-appropriate name for a leader of nomadic invaders, the devs admitted that they just wanted an excuse to do a Star Trek II: The Wrath of Khan-parody Skyward Scream.
- Downplayed on King of the Hill where Hank's new jerkass neighbor and main antagonist is named Kahnnote Souphanousinphone.
- Kobra Khan from He-Man and the Masters of the Universe (2002). Ironically, while most races of Eternia are afraid of him, given the reputation of his species, the Snake Men, his own species doesn't respect him much, thinking he's grown soft living so long without others of his kind around.
- Jackie Chan Adventures has the Shadowkhan, demonic shadow warriors that are divided into nine tribes under Tarakudo and his nine Oni Generals, with the tribe composed of ninjas serving Shendu for the first two seasons.
- Tzekel-Kan in The Road to El Dorado is the main villain.
- Shere Khan in The Jungle Book is, if anything, more of a villain than he was in the book.