An aspiring supervillain seeking world domination
- Anti-Villain: Has shades of Woobie, Destroyer of Worlds and Well-Intentioned Extremist. Loses the latter by the end.
- Beware the Nice Ones: He has genuinely good intentions for both the world and in his friendship with Penny, but ends up being pushed far enough by Captain Hammer for him to try to break his rule of Thou Shalt Not Kill.
- Cannot Talk to Women: Or at least to Penny, mostly because of how painfully, painfully shy he is.
- Card-Carrying Villain: His alias as well as his slogan ("I have a PhD in horribleness") are an admission of his villainy.
- Clark Kenting: Dr. Horrible's outfit is Billy in a labcoat and goggles. Backfires on him when Captain Hammer recognizes Billy at first glance.
- Deadpan Snarker: "Wow, sarcasm. That's original."
- Even Evil Has Standards: He refuses to commit murder until Captain Hammer boasts that he will sleep with Penny just to spite him.
- Everything but the Girl: Billy gets money, fame and acceptance into the Evil League of Evil but only because the girl he loves dies.
- Evil Costume Switch: In act I, when he changes in his Dr. Horrible outfit. And at the end of act III, when he dons his new red and black costume.
- Evil Laugh: He has a voice coach for it. By act III, he's finally got it.
- From Nobody to Nightmare: Goes from Well-Intentioned Extremist to full on villain. See Not-So-Harmless Villain for more.
- Goggles Do Nothing: He wears a pair, but they don't seem to serve any sort of purpose other than looking cool.
- Hero-Worshipper: Inverted. He evidently has deep admiration for Bad Horse, which Penny finds disturbing when he accidentally mentions it.
- Ineffectual Sympathetic Villain: Until the end, when he joins the Evil League of Evil.
- Jumping Off the Slippery Slope: Or Slowly Slipping Into Evil in this case over the course of the musical.
- Knight of Cerebus: Becomes one by the end of the musical. He even lampshades this.
- Lonely at the Top: He succeeds in his ambition to join the Evil League of Evil but looses the girl he loves in the process.
- Loose Lips: Turns out Captain Hammer and the LAPD are among his listeners.
- Love Makes You Evil: In a strange sort of way because Penny was also his Morality Pet. When she died, so did his conscience.
- Mad Scientist: Deconstructed somewhat, but ultimately played straight in the end.
- Missing Steps Plan: He doesn't seem entirely clear how joining the League will help him conquer the world, or have any particular plans for how to use his rule is supposed to bring about the (equally vague) social improvements he justifies himself with.
- Morally Ambiguous Doctorate: He has a PhD in horribleness!
- Never Hurt an Innocent: At first at least. That is, until he joins the Evil League of Evil in the end.
- Noble Demon: Deliberately avoids fatal crimes. At least until the end.
- Not-So-Harmless Villain: Pretty much. He goes from Ineffectual Sympathetic Villain to full on threat in the end.
- Protagonist Journey to Villain: He has one foot in villain territory in the beginning. Captain Hammer certainly doesn't help things though.
- Psychotic Smirk: When he starts singing Brand New Day.
- Sanity Slippage: Due to the inability to deal with the fact that he girl he's in love with is involved with his nemesis.
- Shoo the Dog: Tries to get Penny to evacuate the room when he has Hammer frozen and everyone else cowering in fear, as he does not want her see him doing this. Tragically ineffective, and she can only watch in fear, and ends up getting killed when the Death Ray explodes.
- Shrinking Violet: He's shy and unable to talk to the girl he likes until she talks to him first and even then he's visibly nervous
- Stalker with a Crush: To Penny.
- Technical Pacifist: Personally against murder, which he sees as beneath him—or at least, would like to. It seems to be implied that the real reason he won't kill is because he knows it's wrong, but he doesn't wanna admit that, so makes up an excuse about it not being "elegant or creative" enough.
- Tragic Villain: After Penny's death.
- Twitchy Eye: Twitches his eye or blinks when he's nervous. To say it happens often would be an understatement.
- Villain Protagonist: Though he begins the musical as the Designated Villain at worst he goes an emotional downhill that leads to him embracing villainy by the end.
- Villain Song: Three memorable ones. Brand New Day, Slipping and Everything You Ever.
- Well-Intentioned Extremist : He's vague on the specifics, but he clearly thinks that the world would be a better place with him in control.
- What the Hell, Hero?: He calls out Captain Hammer for pushing Penny out of the van's way and into some trash.
- Who's Laughing Now?: In his penultimate number, when he freezes Hammer and has everyone cowering in fear.
- Woobie, Destroyer of Worlds: By the end of the musical.
Dr. Horrible's archnemesis.
- Big Bad: People think of him as a hero, but he screws with Doctor Horrible for the hell of it which forms the conflict.
- Bitch in Sheep's Clothing: Despite being a self-proclaimed hero, he's quite the jerk.
- Break the Haughty: In the end, when he is injured by the Death Ray explosion and is seen crying to a psychologist in the closing scenes.
- Captain Superhero: It's in his name.
- Chest Insignia: Of a hammer.
- Civvie Spandex: His superhero outfit is mostly just normal articles of clothing.
- Cloud Cuckoolander: Even in a cast like this, Captain Hammer says... strange things sometimes.
- Corporate-Sponsored Superhero: Or corporate tool, if you ask Dr. Horrible.
- Create Your Own Villain: If he hadn't been so convinced that all nerdy kids are potential supervillians, he probably wouldn't have to worry about Dr. Horrible.
- Dirty Coward: He's only brave when his powers keep him from being harmed by conventional means. The moment he actually experiences physical pain he immediately flees in panicked tears.
- Drop the Hammer: Averted; despite having the word "hammer" in his name, he's never actually seen using one as a weapon.
- Dumb Is Good: Utterly deconstructed. Advocates anti-intellectualism, telling kids that any kid who's either a nerd or "different" in some ways is a potential supervillain who must be put behind bars. Needless to say, he's a thoughtless jerk who barely even registers on the side of good, and does even more damage with his aforementioned approach by making a monster out of what may have been a non-threat.
- Dumb Muscle: Downplayed in that he's smart enough to follow Dr. Horrible's Blog and immediately realizes that Billy is Dr. Horrible.
- Feel No Pain: Implied when the malfunctioning death ray exploding in his hands causes him pain, or rather, "I think this is what 'pain' feels like!". Apparently, he had never felt pain before.
- Good Is Not Nice: Deconstructed. He's a petty, bullying, anti-intellectual, womanizing smug jerk. He also saves the city from super-villains on a regular basis, but only for the PR, and is completely unconscientious about the safety of its citizens, judging from his "save" of Penny.
- Handsome Lech: He's quite the womanizer.
- Have I Mentioned I Am Sexually Active Today?: "So I thank my girlfriend Penny (yeah, we totally had sex)/She showed me there's so many/Different muscles I can flex..."
- I Want My Mommy!: "Mama! Someone maternal!"
- It's All About Me: The main reason he loves being a superhero is the limelight. Even in his final number "Everyone's A Hero" he sounds utterly narcissistic.
- Jerk with a Heart of Jerk: Penny thinks Captain Hammer is really sweet on the inside, despite being a bit full of himself. The truth is Captain Hammer is only being nice to Penny to get in her pants and simultaneously piss off the eponymous character. Lampshaded when Penny states that he must have a deeper layer that's totally different from the one on the surface, Billy replies that sometimes there's a third, even deeper level, and that one's exactly the same as the top surface level — like pie.
- Kick the Dog: He dates and sleeps with Penny just to spite Billy.
- Knight Templar: Full of himself, nonetheless.
- Laser-Guided Karma: His idiotic handling of Dr Horribles ray gun in the climax ends up turning him into a psychological wreck that needs months in therapy.
- Meaningful Name: The hammer is his penis.
- Miles Gloriosus: He's only brave and bold because he's invulnerable to damage. The first time he gets hurt, he literally runs screaming like a little girl and spends months in therapy over it.
- Manchild: His abrasive nature, promiscuity, hobby of dicking over Dr Horrible any way he can for shits and giggles and complete mental collapse upon being injured for the first time ever show him as little more than a craven bully who hasnt grown out of pushing kids around in the playground.
- Neat Freak: Why he constantly wears gloves. Pay attention to him during the "My Eyes" song and it becomes clear he's hiding it from Penny. Possibly just an extension of his superiority issues over everyone else.
- Nigh-Invulnerability: He only gets injured in the end, from the Death Ray explosion.
- Non-Indicative Name: For a guy named Captain Hammer, he's never once seen wielding a hammer.
- Not So Invincible After All: His First Time Feeling for pain triggers a total mental breakdown.
- Politically Incorrect Villain:
- "I hate the homeless... ness problem that plagues our city."
- "Don't worry if it's hard./If you're not a friggin' 'tard you will prevail!"
- Pride: He has quite the ego.
- Really Gets Around: Has never slept with the same woman twice.
- Science Is Bad: In the spinoff comic, he demands that children report nerds to the police.
- Smug Super: His ego's just a bit too big for his own good.
- Stealth Pun: It's the reason for his superhero name, considering hammers bang stuff (well, people in his case).
- Villain with Good Publicity: Hammer is a crude bully who is more concerned with getting the limelight than the safety of the citizens even as he's saving them, but the public absolutely laps it up.
A volunteer at the Caring Hands homeless shelter and Dr. Horrible's love interest.
- Dies Wide Open: Her final fate.
- Horrible Judge of Character: Fails to see the problems with Hammer as a person. She does catch on, just a little too slowly.
- The Ingenue: And how. She's good-hearted but horribly naive. She does realize what a tool, pun intended, Hammer is, but a little too late.
- Kill the Cutie: Her ultimate fate. Of course, given that it's a Joss Whedon production, many author-savvy viewers saw it coming.
- Meaningful Name: Lots of possibilities. It could refer to her charity and optimism, her being something under valued or unimportant, or a payment for what Doctor Horrible wants in life.
- Morality Chain: For Dr. Horrible. Her death is the final catalyst for his transition into villainy.
- Nice Girl: Her defining trait. The one unambiguously good character in the musical.
- Not Listening to Me, Are You?: Her speech to Billy in act I trails off into "...so they can buy rocket packs and go to the moon... and become florists" when she sees that he's not paying any attention.
- Parental Abandonment: Implied in her prequel comic.
- Stood Up: She waits for Billy in act III with frozen yogurt, but he was busy plotting Captain Hammer's murder.
- Too Good for This Sinful Earth: Penny is the nicest person in the story, and unwittingly causing her tragic death is what sends Billy spiraling into true villainy.
- Trash Landing: Shoved into the trash by Hammer by his save.
Dr. Horrible's sidekick
- Anti-Villain: To some extent, though he seems to have less of a problem than Billy when it comes to killing someone.
- The Dragon: To the good doctor himself, sorta.
- Blessed with Suck: His "Power" is merely that he's perpetually moist and can make other things slightly damp.
- Ineffectual Sympathetic Villain: Played with, given that his boss is actually worse at the whole evil gig.
- Misapplied Phlebotinum: His condition is due to a plutonium-powered air moistener that his father got to fix his dry skin.
- Power Incontinence: Can't control his moisture.
- What Kind of Lame Power Is Heart, Anyway?: The power of moistening is... not the greatest.
- Weird Trade Union: The Henchman's union.
So go kill someone
Signed, Bad Horse"
The leader of the Evil League of Evil
- Animal Superheroes: Inverted: he is a horse, and he's evil.
- Animal-Themed Superbeing: Until the reveal that... he really is a horse.
- The Dreaded: Bad Horse inspires equal parts dread and awe from other villains. And only the former from everyone else.
- The Don: Based on his letters, he's this to the Evil League of Evil.
- Evil Laugh: His terrible death whinny. It apparently set the standard for evil laughs.
- Exactly What It Says on the Tin: He's a horse, and he's bad.
- Greater-Scope Villain: Technically the Big Bad of the show is Billy himself, with Captain Hammer as the Hero Antagonist, but Bad Horse has a greater presence in the setting as a whole. He leads the Evil League of Evil and is the one who pushes Billy towards evil, ordering him to commit murder in order to gain entrance to the League.
- Red Baron: The Thoroughbred Of Sin.
- Small Role, Big Impact: Though he only has a seconds-long cameo at the very end of the video, Bad Horse's high standards for joining the Evil League of Evil are what drives Dr. Horrible to build his freeze ray and set off the plot.
- The Unintelligible: Subverted. Speaks only in horse sounds for most of the ELE comic, with Jefferson claiming that Bad Horse was appointing him "vice president". Subverted at the very end when Bad Horse speaks English.
Evil League of Evil leaders
- Professor Normal: A cyborg with a super strong robotic arm and jaw attachment. Otherwise, he's a normal person with a wife, kids, and a mortgage, hence his name.
- Tie-Die: A hippie-themed supervillainess able to make hippies violent and angry.
- Dead Bowie: A David Bowie-inspired supervillain with the power of persuasion. Claims to be the real David Bowie who was murdered in 1980 and that every other appearance by Bowie afterward was an impostor.
- Fury Leika: Her name is a pun off of "Hell hath no fury like a Woman Scorned." She was left at the altar and then pooped on by a radioactive dove. She gained poisonous flowers, incendiary rice, a ball and chain around her ankle, and four henchwomen each carrying something old, something new, something borrowed, and something blue.
- Fake Thomas Jefferson: Claims to be the real Thomas Jefferson, though that is unlikely unless Jefferson had Super Strength. Also carries a quill pen tipped with tranquilizer. Doesn't like to have lots of stuff in his pockets.
- Snake Bite: A supervillainess with a cobra-themed costume. Carries a staff topped by a mini disco ball. Did not appear in the "Evil League of Evil" comic with the other ELE leaders.
- Hourglass: A villainess who is able to see the future. Tells Moist about a kid who will become President. An unseen character.
- Bait and Switch: A pair of villains who Moist goes on a double date with. Somehow able to fool him into thinking he was dating Bait instead of Switch. Bait is apparently the more attractive of the two.
- Conflict Diamond: A villain friend of Dr. Horrible and Moist. Went on the double date with Moist, Bait, and Switch.
- Pink Pummeler: A homophobic villain with Super Strength, Gaydar, and a superhuman knowledge of Broadway show tunes. Repeatedly rejected by the ELE due to his tendency to date rather than beat up his victims.
- Purple Pimp: A supervillain who appears at the party for Dr. Horrible's induction into the ELE.
- Johnny Snow: An amateur hero not affiliated with the Council of Champions. He wears a parka and carries an Ice Beam. He's mentioned in Act I and appears in the ELE comics, where he foils a plot by the ELE to poison the city's water supply by freezing it. The villains are impressed and mistake him for a supervillain.
- James Flames: A potbellied superhero with pyrokinetic powers. His Catchphrase is "M'name's James and I have the power of flames." Wears a singed T-shirt and pink overalls. He thaws the water supply after Johnny Snow freezes it.
- Wingspan: A member of the Council of Champions, along with Captain Hammer. Works in a command center in the sky. He, along with the rest of the Council, foolishly leaves the city for a retreat, allowing the ELE to wreak havoc. Appears briefly in the ELE comic.
- Elementia: A blue-skinned superheroine and a member of the Council of Champions. Works in a command center with a waterfall and apparently has some kind of Elemental Powers. Has no problem sitting naked in a sauna with men.
- ???: An unnamed member of the Council of Champions with a third eye in the middle of his forehead. He appears in the sauna with the rest in the ELE comic.