The entirety of the Gedou Otome Tai from Akahori Gedou Hour Rabuge. While they're daughters of low-ranking mooks from an evil organization, their ability to actually do anything evil is zero.
Shia in Pita-ten is the epitome of this trope; as demon she's not only supposed to do evil, she *has* to do evil, but she always seems to wind up baking cookies for everybody, or cleaning up the apartment she shares with Misha (an angel almost as bad at doing good as she is at doing evil), or just in general being polite, soft-spoken and helpful, much to the exasperation of her demon-adviser in cat form, Nyaa.
DojiDevil, a one-shot character in the Hot Springs Episode of Kyouran Kazoku Nikki, always on cleaning duty as punishment. She was trying to find whoever was fated to die at the springs (it ended up being a Self-Fulfilling Prophecy) so she could steal a soul and gain recognition, but was so touched by them that she spent most of her time cheering them on and trying to help them. She finally sets up a plan to kill them all so the family won't be separated but regrets this almost immediately.
Shiyu Kusanagi in the X/1999 manga, CD Drama and TV series. What is a Gentle Giant who goes out of his way to help other people (including his enemies!) doing in the humanity-destroying Dragons of the Earth group?
Demon God Ifurita in the TV series version of El-Hazard
Chachamaru on Mahou Sensei Negima! is technically a villain because she's trying to kill Negi, but that's only because she's following her programming. When she's not doing that, she can be seen retrieving lost balloons for little girls, helping old ladies across the street, and rescuing stray cats.
In Ratman, the minions of Jackal, who wear spooky skeleton outfits, in the first chapter forget they were supposed to kidnap Shuto. So they instead played with and fed stray kittens.
Antylamon, the last of the 12 Devas in Digimon Tamers. While the other Devas would usually attack humans on sight, Antylamon doesn't attack or threaten Suzie, the first human she meets, at all. Suzie even makes her do a Heel Face Turn, as she not only defends Suzie from Makuramon, but becomes her partner.
Android 16, in Dragon Ball Z. He was created for the sole purpose of destroying Goku, and refuses to fight anyone but him. He also takes an interest in birds and squirrels, and loves the world so much that the only character in the series he does try to kill is Cell.
Vizzini: Finish him! Finish him, your way. Fezzik: Oh goody, my way. Thank you, Vizzini... which way is my way? Vizzini: Pick up one of those rocks, get behind a boulder, in a few minutes the man in black will come running around the bend, the minute his head is in view, hit it with the rock! Fezzik: My way is not very sportsman-like.
Zangief from Street Fighter probably fits this. He has a Heel Face Turn when someone informs him that Bison is the bad guy.
It was Deejay. And why was Deejay evil? In his own words "because I'm being paid a damn fortune!". Zangief wasn't paid like Deejay was causing his turn.
Not quite - he legitimately thought that General Bison was the good guy, and that the forces of evil and oppression were against him because of it.
Doc Hopper's assistant, Max, from The Muppet Movie warned Kermit about Hopper's plans.
Administrative Assistant Bob from Demolition Man isn't actively evil... he's just trying to help out whoever is in charge. (It's his job to help, after all.) This is why he can go from working for Doctor Raymond Cocteau to working for Simon Phoenix to working for Edgar Friendly without once ever batting an eye.
Hopper's brother Molt in A Bug's Life. While Hopper is malicious, cunning and depraved, Molt is... not.
Hopper:(to Molt) I swear, if I hadn't promised mother, on her death-bed that I wouldn't kill you, I would kill you!
Jenner's best friend and minion Sullivan from The Secret Of NIMH isn't really a bad guy at all, he just didn't choose his friends wisely. When Jenner plots to kill Nicodemus and Mrs. Brisby's children he objects to this, which leads to his Heel Face Turn. Unfortunately, before he can officially join the heroes, he is stabbed in the back and mortally wounded by Jenner for interfering with his plans... but before he expires he pulls a Redemption Equals Death when he throws a dagger into Jenner's back and kills him... with his last dying breath.
From Tombstone - Mc Masters, Texas Jack Vermillion, and Turkey Creek Jack Johnson don't mind robbin' and stealin', but don't like messin' with the women for the evulz. Also Deputy Billy Breckinridge thinks there has to be some law.
From The Sorcerer's Apprentice: Drake Stone, an arrogant Morganian turned celebrity illusionist, is recruited by Horvath to release Morgana, but he never does anything that evil. It's pretty clear that Drake starts to feel incredibly uncomfortable with the consequences of his actions, especially when Horvath implies that children will die for his cause.
Evil's assistants in Time Bandits are all pretty dim and full of useless suggestions.
Literature
Smee, Captain Hook's bosun in Peter Pan, as well as its many adaptations.
The Mistmantle Chronicles has this in the form of the female squirrels Crackle and Gleaner. To quote, "Crackle seemed to go out of her way to make trouble, while Gleaner seemed to do it naturally." Crackle quickly becomes part of the supporting cast and one of their friends after she comes to work at the tower as a cook, also partially upset that Gleaner has basically forgotten about her while serving the Big Bad's wife, Lady Aspen.
The children's book Which Witch? features Belladonna, who tries her hardest to be an evil, hag-faced black witch like all the rest. Unfortunately her natural tendency is that of a Purity Sue-level white witch that makes all the other witches feel sick.
Draco Malfoy from Harry Potter. For the first five books, he was a Jerkass who never got closer than Red Herring to being a real villain. When he was finally given an important job by the bad guys in Half-Blood Prince, it quickly became clear that he couldn't do real evil; he tried to kill Dumbledore indirectly but all of his attempts failed. When he finally had a golden opportunity to kill him on the spot, he couldn't go through with it, and only disarmed him. The only reason he tried to go through with it was fear of what Voldemort would do to him and his family. Oh, and Dumbledore was perfectly aware of what he was up to the whole time, but didn't approach him for fear of Voldemort catching on through Legilemency.]
Also in Deathly Hallows, when the trio are caught and brought to Malfoy Manor, and Draco is asked to take a look at them to see if they've got the real Harry Potter, he clearly knows it's them, and is clearly reluctant to identify them, since he knows that doing so will ensure that Voldemort will come and kill them.
Live Action TV
Doctor Who has plenty of examples, most recently Luke Rattigan in The Poison Sky, who thinks the Sontarans killing people with his inventions is cool but lacks the nerve to get his own hands dirty and ultimately sacrifices himself so the Doctor won't have to.
Davey in the pilot of The Sarah Jane Adventures. This is the guy who refuses to follow Maria and Luke into a womens' bathroom, because "That room is designated for females only. We are males... this culture says we must never go in."
Well, if you overlook the "murdering a girl in cold blood" thing or the fact he seems to hate Bajorans even more than his boss... He's actually more of a Dragon Ascendant who does a Heel Face Turn.
Garry and Grahame in Maid Marian and Her Merry Men. They're inept to the point Marian and co quite like them when they're not pursuing them on Nottingham's orders.
The guards in Robin Hood, meanwhile, turn out to have a C- In Evil. They won't obey orders to strike down unarmed peasants during a sit-in, but as soon as it turns into a proper fight they're right back in the game, even though it's still mostly a proper fight with unarmed peasants.
Sgt. Schultz from Hogan's Heroes is often seen a a bumbling underling to Colonel Klink, and unlike most of Those Wacky Nazis, he is willing to turn a blind eye to Hogan and his crew's antics.
Schultz basically knows everything that everyone is doing, knows whether they're bad or good, is hyper-effective when he needs to be, and is a cheerful fat man who made toys for the little children before the war. Yes, it's true, the Nazis drafted Santa Claus.
Joxer's first appearance in Xena: Warrior Princess had him working for the villain Callisto. Gabrielle pointed out that he just wasn't cut out for evil. He later pulled a Heel Face Turn, becoming an earnest (and somewhat less incompetent) hero.
Ares' bumbling sidekick Strife, despite being a god, was a similarly incompetent character who never really caused trouble or meant anyone harm, and was constantly bullied and insulted by Ares for it. Ares did mourn for Strife, though, after Callisto killed him with a god-slaying weapon...
Ares (visibly shaken): He wasn't so bad. He tried hard. He... he was just no good at his job.
Post-vamping, Brainless Beauty Harmony of Buffy the Vampire Slayer wanders into this trope a lot. Most famously when she deeply apologizes for not noticing a "No Smoking" sign. She wants to be evil, but like everything else, she's just really bad at it.
Buffy: Harmony, when you tried to be head cheerleader, you were bad. When you tried to chair the homecoming committee, you were really bad. But when you try to be bad? You suck.
Rusty the Tow Truck in the preschool series The Big Garage. In fact, in every single episode, he always joins the cast for the final song of the episode, and leaves the garage just before the credits roll.
Radio
Scumspawn in the BBC Radio 4 comedy series Old Harrys Game. He is a demon, one of Satan's chief minions, and much is made of his disgusting physical appearance. He also donates to donkey sanctuaries, is a supporter of Friends of the Earth, is often exceedingly kind to the damned, and has a chaste but touching love for his master.
Theater
Lola from Damn Yankees, who fails miserably at playing her role. Nothing disgusts Applegate more than having The Vamp sympathize with the man she is supposed to seduce.
Sir Ruthven Murgatroyd (alias Robin Oakapple) from Gilbert and Sullivan'sRuddigore. Despite hiding from his inheritance of the title of Bad Baronet of Ruddigore (and the related curse that would force him to commit a crime a day or perish in terrible agony), he is discovered and pushed into the role. The problem is, he's not really very good at committing crimes and many of his attempts end up being more rude than fiendish. When the disgusted ghosts of previous Bad Barons exhort him to at least carry off a lady or something, he protests that he "isn't that kind of Bad Baron!" They have to give him a taste of the terrible agony to prod him into it.
Video Games
In fandom, Demyx, the magical sitar player of Organization XIII is either an example of this trope or an incredibly scary and evil Crouching Moron, Hidden Badass. In the game itself, he carries cue cards with his mission on them, and his first line is "Run! Run away!"
358/2 Days expands on this. He now bribes Roxas to do his missions for him and chats gleefully about how being lazy saved him from getting killed at Oblivion.
Johnny Sasaki in Metal Gear Solid 2 and his identically named and voiced grandfather in Metal Gear Solid 3. While just incompetent in 1, he progressed to the point of making friendly conversation with the people he's on patrol for in 2, and his grandfather even shows family pictures to the people he's guarding. Oddly enough, becomes a major character and Took a Level in Badass in 4.
The Koopa Kids from the Mario Party games do this from time to time. One would take coins from players, but occasionally would give coins instead, then realize his mistake and leave anyway.
Balrog from Cave Story is only a villain because the Demon Crown compels him to obey the Big Bad. When nobody's looking, he's cheerful, helpful and even saves Quote and Curly Brace from the Load BearingBonus Boss Ballos.
In the final case of the Phoenix Wright trilogy of the Ace Attorney series, there is a character who receives instructions to help with a murder and is so innocent as to misinterpret them as instructions to throw gravy onto a portrait. The same case also involves a Purity Sue who is absolutely committed to helping protect both a Complete Monster and a Sympathetic Murderer and following any instructions from them regarding how to help them avoid being caught.
Web Comics
The Monster in the Darkness from The Order of the Stick, who manages to spend most of an epic battle scene having a tea party (to be fair, he wasn't asked to do anything to actually help), and constantly fails to grasp the main plan of the villains. He even gets a Crowning Moment of Heartwarming with a captured paladin which causes one to wonder if he's even trying to be evil.
He later saves said paladin (named O-chul) and Vaarsuvius from death via ingested meteors. He teleports them away and Xykon doesn't even realize it was The Monster in the Darkness who did it.
Thog from the Linear Guild has elements of this as well. Though he's actually very good at killing people, he's too stupid to realize that this is bad and would be equally content eating ice cream or playing with a puppy (or whatever poor bystander he can force into the role of the puppy). He's shown to be largely harmless without his boss Nale to goad him into evil, though with Nale around he does better (worse?).
I dunno, he did come up with subjecting Elan to Celine Dion on his own, something that even Nale found reprehensible.
This very debate is lampshaded by Roy when they fight in the arena.
8-Bit Theater features so many subversions of standard hero and villain roles that this trope inevitably shows up, most notably with Garland, who can't seem to grasp that offering the goodguys cupcakes is not proper behavior for a wannabe Evil Overlord. It's so bad that his captive, Princess Sara, has to help him be evil. The rest of the Dark Warriors are hardly any better: Bikke makes Ralph Wiggum look bright (his worst "crime" is getting his entire crew killed by being too cheap to feed them), Vilbert is a Goth vampire who thinks he's in a LARP, and Drizz'l might be a threat except that he's forced to play Only Sane Man for the other three idiots.
This is also inverted, as the most effective villains in the entire story, by atrocities committed, are the Light Warriors, of whom Fighter is the only actually good member (maybe). He fails to be evil so thoroughly that he genuinely believes that he and his murderous, sociopathic friends are the good guys.
The Light Warriors fall into this a lot—not because they're not evil enough, but because they're too stupid to do it right.
During the "That Which Redeems" story arc from Sluggy Freelance, the Dimension of Pain demons start turning people in the Dimension of Lame into demons as well. However, as one demon puts it, "When you start with wussie mortals you get wussie demons."
Much later on, a journey to the Earth's surface to rescue Gloog from the main characters instead results in him being forced into helping and then being beaten senseless by a senile old woman.
Jurinjo from Emergency Exit is amazing at this trope. He helps Eddie buy groceries, delays reporting back from a mission until he eats ice cream and sees a dancing monkey, shows the heroes the location of a Plot Coupon, has doubts about continuing to work for the villain, doesn't want to attack an opponent who seems to be less well armed then he is, is upset when another villain attacks one of the heroes , offers to heal the hero and has to be reminded that villains usually asks for payment, and actually holds up his end of the deal and seems to be making friends with one of the heroes.
To a lesser degree, Orulla.
Dr. Kinesis' minions in Evil Plan, who seem to think that Kinesis' cruelty is simply the way their leader shows them he loves them. Hint: It isn't.
Fuchsia from Sinfest is well on her way to becoming this after crushing on Criminy. Now, instead of tormenting the souls of the damned, she reads them stories and sings comforting songs to them.
Wilson and especially Pickett, Notfunny Cartoons' resident mad scientists. Examples include the Killbot 5000, who works as a kindergartener because he couldn't bring himself to hurt a soul, or the genetically engineered werewolves, which would be fine if they didn't keep on coddling rather than killing. At one point, Wilson accuses Pickett of not being serious about this whole "evil science" thing. Pickett quickly pulls out a remote with a big red button, saying he's not sure anymore what it does, but if he recalls correctly, it should be something very bad. So Wilson presses it. A split second later, the phone rings. When they pick it up, the response is "Something very good just happened. Thank you."
Evil Diva: The title character. Even when the school sends home a letter to alert her parents to how good she is acting, she can't help herself but help a kitten caught in a tree.
Richard from Looking for Group got hauled in front of a court of his (evil) peers because he'd become a minion to protagonist Cale. Eventually he got bored and, shall we say, opted out of the proceedings.
Homestuck: The Courtyard Droll, and by extension his troll's session counterpart Clubs Deuce. He gets close to John, who creates for himself an Infinity Plus One Hammer, and what does he do? He high-fives John. Being incredibly moe and something of a Shrinking Violet doesn't help his case in the slightest.
He does try though: after being sent on a mission by John with the uberbunny and WV, he gets the idea to steal the wallet John gave WV. He then escapes and contacts his superior, Jack Noir. Unfortunately for him, that wasn't his mission in the first place, so he gets barked at. He then goes and actually does his mission, which was to kill Jade. Because of Jack Noir's feelings for Jade he inherited from Becquerel, he kills the Droll and sets up Jade's resurrection. Poor Courtyard Droll.
Web Original
Heartbreaker and Jello of The Masterminds, in the Whateley Universe. They seem a lot more interested on protecting their friends than in actual villainy.
Western Animation
Kronk from The Emperor's New Groove doesn't quite get the villainy thing. Not so useful, since he's Yzma's only henchman.
The Grubs are too dim to be properly evil-when quizzed on what they hate most about Buzz, they say, "I donno. He seems like a pretty nice guy." The Brain Pods are better at it (since their purpose is pretty much to be smart) but the thinking aspect is pretty much all they're good for.
Stormer on Jem; a few episodes even dealt with the fact.
The best known being the one where she and Kimber form their own duo group; Stormer only returns to the Misfits because she cares too much to let her friends utterly fail, which they would without her.
Hack and Slash from ReBoot, who are dismayed when Bob is lost in the Web and unable to keep them from doing anything really bad, like killing others. Though, considering their level of competence following their Heel Face Turn, they also have an F in Good as well.
Senor Senior Jr. on Kim Possible. His father, Senor Senior Sr., took up villainy as a hobby after retiring and often ropes his son into acting as an accomplice in his schemes. Senior Senior Jr. has no interest in villainy and would much rather be a boy-band singer.
Which may or may not be just as bad depending on your point of view.
Guild henchmen from The Venture Bros. (except for the Guild Blackout squad sent to assassinate the Venture family under orders from Phantom Limb) In fact, the typical henchman is more along the lines of a Punch Clock Villain than a true servant of evil. Guild henchmen are portrayed as ordinary civilians who just chose an atypical line of work, and thus most of them can't really comprehend their boss' schemes. They can and are used as deadly tools of the supervillain's mastery, but are more typically comfortable with engineering or secretarial positions, or just tag along with the supervillain as he or she live their own lives.
Numbers 21 and 24, employed by the Monarch, especially fail at evil. If they took an evil test, they would not likely get more than a 10%. They are generally useless in combat, have little strategic ability, and they spend their time bickering over fantasy fistfights instead of actually participating in villainy. Their Genre Savy ability is beyond compare though, making them in the words of the Monarch, "That special mix of expendable and invulnerable", which is how they survive for so long; they know being evil/loyal is the fastest way to die by Brock's hands.
21 completely subverted this in the fourth season after witnessing 24's murder/accidental death when he Took a Level in Badass by completely whipping his body and selfdiscipline into shape and becoming "General 21", a highly trained, merciless supersoldier. However he still does not fare very well in the evil department, as he completely fails to torture Hank and Dean and even openly admits to them that he cannot tap into his inner hatred the way the Monarch can.
Their own boss The Monarch has his own incompetent moments as well. When discussing his arching plans with Monstroso, he suggests "coating the Venture compound with honey so he's devoured by ants and jiggers" and then "stick him in a bag and beat him with a rake." Monstroso shoots down both plans as being stupid.
