Obito Uchiha from Naruto is essentially the Darth Vader of the series. He aspires to become Hokage, gets crushed by a boulder, is saved, trained, and manipulated by an elderly Madara, is turned to the "Dark Side" after witnessing his love interest's death (even was able to foresee it through the eye he gave to Kakashi), then wears a mask (which deepens his voice to boot), discards his old identity for Tobi/Madara, and then goes on to terrorize the ninja world. He eventually gets defeated by Naruto and is redeemed by both his and Kakashi's words, and even turns against his godly-powerful master to boot. Fortunately, he has had more opportunities to do good than Vader did. Even after he finally dies, he manages to Kamui his spirit back to the real world to assist Kakashi, essentially making himself a Force Being.
Hanzo of the Salamander wearing a semi-covering mask and have rather prideful personality that resembles a ninja version of the Star Wars villian himself.
Cade from Star Wars: Legacy refuses to let his childhood love Azlyn die, even though she asks him to, accepting her fate and the will of the Force. When all other options fail, he gets her to people who put her in a Vader-esque life support armor. After waking up, she was really pissed at him. Fortunately for her, she managed to avoid slipping to Dark Side and managed to get the scary black suit replaced with something much more elegant. One of the doctors was reluctant to put Azlyn in the armor out of fear of creating another Vader. Someone else pointed out that Vader turned evil before he was put in the suit.
Darth Krayt also has several Vader-esque qualities, most obviously his appearance (he's big and imposing, and his armor is dark, spiky and includes a face-concealing helmet) his backstory (fallen Jedi turned Sith Lord), the fact that he's suffering from a crippling physical condition which his armor helps abate, and his interest in turning the protagonist. However, he's the Big Bad, not The Dragon (and ironically, his Dragon, Darth Wyyrlok, is in many ways more like Palpatine than Vader).
The Enlighteneds from Valerian album, The Empire of a Thousand Planets are another example that actually predates Star Wars and may have played a part in inspiring it. They are a mysterious sect of seers who hide behind ominous metallic masks and their leader has a dramatic unmasking scene where he reveals himself to be a human being scarred and deformed by cosmic radiation.
Darth Maul is obviously an Expy of Darth Vader in a The Dragon sort of way. Count Dooku is also an Expy of Darth Vader, but he's actually got more in common with The Emperor. General Grievous is a bit closer to Vader; Darth Vader has trouble breathing, Grevious has a cough, and they're both cyborgs. Word of God says the three were used for foreshadowing, each one being an element of Vader: Maul as The Dragon who enforces the Emperor's will, Dooku as a fallen Jedi, and Grievous as a cyborg with breathing problems.
Darth Vader's own appearance is often thought to be inspired by the Film Serial character The Lightning from The Fighting Devil Dogs.
Captain America: The Winter Soldier - If the title villain wasn't one in the comics, he fits the bill here. Ridiculously dangerous cyborg? Check. The Heavy for a less physically-imposing villain? Check. Ominous black mask? Check. Fallen Hero? It's an eight-year-old spoiler to anyone familiar with the comics.
Margaret Weis is a huge fan of the Vader character, so it's no surprise she borrowed his general aesthetic for several of the Dragon Highlords from the Dragonlance Chronicles, which she co-wrote. The closest to Vader in terms of both appearance and character, though, is not a Highlord at all, but rather the undead knight Lord Soth. The direction of Raistlin's story arc also paralells Vader's in some ways, though the two characters aren't very alike in terms of personality, appearance, or abilities.
Weis also borrowed heavily from Star Wars for The Star of the Guardians, in which Derek Sagan has a cape, a really deep voice, betrayed his order and his loved ones due to pride, overthrew the old authority, and you can probably fill in most of the rest of his character arc just from the name of this page.
The Red Haired assassin in The 15 Keys has a very Darth Vader feel about her, even wearing the right armour for the job. The 15 Keys author is a huge fan of star wars, with Darth Vader as his favourite character and so wanted to make one of the Darth Vader clones. Another Character who fits this discription in The 15 Keys is Toby, but he is not villainous
The Star Wars Expanded Universe has a lot of books taking place after Vader's death, and a number of villains who call back to him, even if they'd never met him. Kueller of The New Rebellion is one of the most notable ones, though he also has callbacks to the Emperor. There's even a point where Luke, fighting him, decides to have an Obi-Wan Moment and let himself get killed so he can guide his sister - but his sister interrupts by just shooting Kueller.
In the New Jedi Order, Nom Anor is clearly Genre Savvy about Vader's reputation and deliberately invokes this trope in his dress and mannerisms when confronting Leia in the first book. Subverted in that as we get to know him better it becomes obvious that, apart from both being villains, he's not really much like Vader at all.
Galaxy of Fear has a literal clone of Vader, dressed in what's described as a cheap knockoff of Vader's armor. He's more petulant and unskilled than the real thing, too.
Jacen Solo in Legacy of the Force is constantly compared to Vader, for several reasons: the obvious one (he's Vader's grandson); he deliberatly adopts several of Vader's practices once he assumes command of the Galactic Alliance Guard (which has many similarities itself to the 501st Stormtrooper Legion, aka Vader's Fist), such as fighting on the front lines; he dresses almost exactly like him, in black armor, later with a black cape, more than one person notes "all he needs is a black helmet" and he'd be the spitting image of Anakin Skywalker; and finally their personalities, philosophies, driving motivations and so on are identical in almost every aspect. Later on, he also adopts Vader's "signature "force choke the failure/source of my displeasure" attitude, culminating in him accidentally killing a subordinate in anger. It really doesn't help that his character arc in the novels was meant to mirror his grandfather's.
Glen Cook tells a story about when he was trying to sell the first Black Company book early in the late 1970s. Publishers did not want it. Along with the manuscript, he had some character paintings a friend of his had prepared, although Cook did not use them in his proposals. One pictured Soulcatcher dressed in black leather and a mask and morion. At a SF convention, an editor happened to see that particular illustration and thought "Darth Vader!" He bought the book based soley on the picture and offered a contract to Cook's painter friend to paint book covers. Other than this superficial resemblance (and the common trope of both being Dragons who plot against their Big Bad), the character of Soulcatcher has no resemblance to DV.
Nefrai-keshnote formerly known as Lord Kenwick Norrington, leader and most powerful of the sullanciri from The Dragon Crown War series is a definite example, fitting almost all of the criteria. He's the Big Bad's Dragon, a Fallen Hero, related to The Hero (grandfather rather than father, though), a Magic Knight (always a powerful warrior, and acquired powerful magic after becoming a sullanciri), wears a cloak and a succession of creepy masks (actually a sign of prestige in his homeland; his non-villainous countrymen wear them too, though Nefrai-kesh's tend to be especially sinister) and has something of a Noble Demon streak, with the implication that he was deliberately holding back so as to sabotage the Big Bad's forces without her knowledge. He also has something of a "Vader and Obi-wan" relationship with the supporting character and mentor Tarrant Hawkins/Crow, with the twist that he was Crow's Big Brother Mentor, rather than the other way around, before his Heel-Face Turn. Perhaps unsurprisingly, the series' author, Michael Stackpole, has written many works for Star Wars.
Wolzard from Mahou Sentai Magiranger. Heavily-armored, deep-voiced, sword-wielding black-magician dragon to the Eldritch Abomination N.Ma - and secretly the team's brainwashed missing father. His Mystic Force counterpart Koragg also counts, although he's only the Red Ranger's dad.
Before either of them was Chouryou/Iron Face Xiang Lao from Gosei Sentai Dairanger. Fallen Hero and father of Ryou, the series' Red Ranger. He is by far the most blatant. His boss amongst the villains is a ripoff of the Emperor when in human guise, he dies saving his son from said boss's Electric Torture, and the spirits of his friends appear to forgive him when he passes.
Curiously, this series also has a Suspiciously Similar Song based on... the Imperial March, which is associated with Vader. However, Chouryou is only around for 9 episodes in the beginning and the song is still used for the villains for the remainder of the series.
Scorpius from Farscape is a super-strong, deep (natural) voiced high-ranking enforcer for The Empire who wears a black outfit with life support functions.
The Cigarette Smoking Man from The X-Files is The Dragon to the higher ranking members of the conspiracy, is in ill health, wears dark clothing, and is trying to bring Mulder over to his side. He also claims to be Mulder's father.
A non-canon example is in The Force Unleashed's dark side ending, which has Galen Marek in a similar situation to Darth Vader by being made a cyborg.
Death's Hand in Jade Empire takes this trope back to the East Asian armor Darth Vader's mask was based off of.
Golbez from Final Fantasy IV is a more fantasy-themed version, complete with a Cecil I Am Your Brother moment. He wears black armor, is a Badass Baritone when he's voiced, has a rather ominous and rather badass theme whenever he is nearby, used to be good but was corrupted and brainwashed by Zemus, and once he comes to his senses he helps the heroes destroy him. In the English versions of the DS remake of the game as well as Dissidia, his English voice actors even voiced him in a similar manner to Vader.
As two more Shout Outs, in Dissidia: Final Fantasy he has an attack called "Cosmic Ray", which fires blasts of electricity from his hands in a manner heavily resembling Force Lightning (ironically, the original Darth Vader could not learn this attack because of cybernetics and is in fact was killed by it), and he calls the CPU boss from IV to fire lasers, the CPU greatly resembling the Death Star as a large black metal Attack Drone.
Gabranth in Final Fantasy XII is The Dragon to The Emperor, Vayne, is revealed to be Basch's Evil Twin and is a Fallen Hero who is pretty much single-handedly responsible for the fall of Dalmasca and the Empire's reign in the region. Clad in dark silver armor with a black cape and having a metallic echo to his voice due to his helmet, Gabranth is actually a broken man who feels he has nothing to live for except his servitude to Vayne, his home and family having been taken from him or given up. By the end of the game he helps the heroes defeat Vayne, but is mortally wounded for his heroism and dies soon after.
Even earlier than both Golbez and Gabranth was Leon from Final Fantasy II. Both were high enforcers of the Empire and second in command to the Big Bad Emperor, both also had former ties to the Main Protagonists by familial relations (although in Leon's case, the term "familial" was used loosely, as the main protagonist was adopted by Leon and his sister Maria's parents), both wore dark armor, and both eventually pulled a Heel-Face Turn with implied guilt towards their atrocities beforehand to take down the Emperor.
King K. Rool behaves this way in Donkey Kong 64. He speaks like the Vader and has Vader Breath. He also has a ship with a huge gun (the Blast-O-Matic, not the Death Star), and he threatens his minions (with Klaptraps, not the Force choke).
Darth Malgus in Star Wars: The Old Republic. Also, most Sith Warrior PCs can give it a decent go, especially with some of the late game helmets like this. Indeed, it's quite common for Sith Lords to wear dark robes, armor, and full masks/helmets.
The bosses of the 1987 Star WarsLicensed Game for the Famicom are a long line of Darth Vader knockoffs, such as Scorpion Vader and Wampa Vader, who drop their masks and cloaks soon into the Boss Battle. The actual Darth Vader is defeated before the assault on the Death Star.
Xemnas from the Kingdom Hearts series in terms of appearance and backstory. He wears a black cloak, has a deep voice, wields "ethereal blades" that resemble red lightsabers, occasionally shoots lightning and no longer responds to his old name. The parallels run even deeper when you connect him to Birth By Sleep. Terra is an Anakin Skywalker clone, following Anakin's fall to darkness in Episode 3 pretty much step for step, diverging from Anakin when Master Xehanort reveals his true colors, fighting him instead of joining him. However it's too late, his heart is consumed in darkess and Master Xehanort bodyjacks him, creating a younger Xehanort. Xehanort battles Terra's friend Aqua, but when defeated he resorts to sealing his own heart to prevent Terra from Fighting from the Inside. This seals his memories, and eventually the reborn Xehanort is split into Ansem and Xemnas, bringing the Darth Vader parallels full circle with Xemnas.
The Gamecube game Custom Robo has Sergei, who not only possessed a baritone voice (well, it's implied due to the eight-bit speech sounds being deep), a face mask obscuring all but his right eye, being a high-executive to the Z-Syndicate, and The Dragon to Oboru, but is also the older brother of Marcei. Likewise, he also pulls a Heel-Face Turn late into the game.
Von Bolt from Advance Wars Dual Strike was a man clad in black who is on life support, although his overall personality traits are closer to Voldemort or Palpatine. Nintendo Power even lampshaded this by stating that his need for a life-support suit reminds some players of a certain Skywalker.
The Masked Man in MOTHER 3. Dressed mainly in black, wears a Cool Mask, is a cyborg, he has his own Laser Blade, and he's The Dragon to King P. And is revealed to be Lucas's brother, Claus. Ironically, his outfit/helmet more resembles a Rebel pilot uniform.
The Black Knight from the Fire Emblem Tellius duology, complete with being a former student of Ike's father/mentor and the one who kills said father/mentor and having an ominous march theme.
Solidus Snake from Metal Gear Solid 2. He arrives on scene wearing a long dark cloak, underneath which is a suit of darkly colored Power Armor, which includes a partial face-shield. He is later revealed to be a former henchman for The Patriots, the brother of Solid Snake and the adopted "father" of Raiden. Later, he reveals his intentions to break away from the more-evil Patriots, commands a super weapon with city-destroying weaponry and "father" and "son" have a final sword duel on top of Federal Hall.
The Warcraft franchise has some contenders.
Arthas fits many traits of this trope when he was still a death knight. He used to be a Paladin and fell to the dark side trying to protect the kingdom he loves. He is also a magic knight and his character model in Warcraft 3 also wore a cape. Arthas also served the Lich King Ner'Zhul, which fits the trait of the physically superior warrior serving a more magically powerful Big Bad.
Later on, Arthas fuses with Ner'Zhul, playing the mask, armor and voice traits of this trope straight. The Lich King wears ornate armor at all times that functions as the magical equivalent of a life support system as well, maintaining his undead status. As putting the armor on literally made Arthas into the Lich King (by merging him with the soul of Ner'zhul, who was made into the original Lich King). In World of Warcraft, he never appears in the actual game or cut scenes without the full armor.
While not quite available as of this writing, Garrosh looks to be something of the sort because of being taken by the Shaa in Mists of Pandaria.
Legate Lanius fits this role better as the heavily armoredDragon to Caesar who also speaks in a deep voice. While he's much less sympathetic, he's at least capable of being reasoned with to some extent.
Zant from The Legend of Zelda: Twilight Princess. Menacing black robes and helmet. Check. Makes a distinctive breath-like sound. Check. Breaks down a door with his underlings, massacres some good soldiers, and captures a princess. Check. Fights with swords and magic powers. Check. Has a semi-sympathetic backstory. Check. built up as the main antagonist only to be revealed at the last second to be working for Ganondorfa Man Behind the Man. Check.
Ninja Gaiden Black/Sigma has Doku, a deep-voiced flaming specter clad in a suit of black samurai armor who is The Dragon to the Vigoorian Emperor.
General Tarquin from The Order of the Stick. He's masked when the heroes first meet him, he's Elan's father (and genuinely cares about his son), and he's ostensibly the second-in-command (and actually the head) of an evil empire. Many, many Star Wars references are made. Unlike Vader, however, Tarquin was never a hero and his love for his sons turns out to be entirely conditional.
Incidentally, (or not), his voice actor in the 2012 series, Kevin Michael Richardson, also voiced Dark Laser in Fairly Odd Parents as mentioned above.
Ben 10's Arch-EnemyVilgax was described by his creators as "Darth Vader, without the sense of humor". However, the similarities are rather limited; other than the deep voice and (in the original show) the life support, Vilgax actually bears more similarities with Darkseid than Darth Vader.
Eon from Ben 10: Race Against Time, on the other hand, clearly is one: he bears a dark armor with a helmet that cover his face, has a deep voice, is the Big Bad of the movie and has to an extent sympathetic motivations in the movie (his goal is to help his species escape extinction, which he intends to do by bringing them on Earth). His appearance in Ultimate Alien puts it even further by revealing this version actually is an alternate version of protagonist Ben Tennyson.
Not only that, but he also gains lightsaber-wielding Mooks.
Scaredy Squirrel gives us The Eeyore of the show, Nester. He bullies scaredy for no reason but leaves him alone when Scaredy becomes a Villain Protagonist of an episode & still bullies him in a future episode. However, he has no woobyist origin story of how much pain the Scaredy gives him. He's also the son of the Bigger Bad.