Mother? May I call you mother? My mother was a person with no self-respect of her own, so she tried to take mine. Ten years old, she had the scissors, you wouldn't believe what she did with those...(chuckling) She's dead to me now. Mostly 'cause I killed and ate her.
In Fruits Basket (the manga, at least; the anime didn't get this far), Akito's issues stem from the fact that her mother insisted that she be raised as a boy out of insane jealousy.
Seishirou's relationship with his mother in X1999. This would be the incestuous kind.
The manga version of Chrono Crusade reveals towards the end that Aion's Start of Darkness was when he learned the Awful Truth that Pandaemonium, the mother of all demons is actually the corpse of a human woman who was kidnapped by demons and grafted onto what was left of the former demon queen—oh, and she was pregnant with twins, who would grow up to be him and his brother, Chrono. This is foreshadowed earlier on in the manga by the fact that he's obviously quite obsessed with and terrified of Pandaemonium.
Ritsuka's mother has been an abusive version of The Ophelia ever since her older son died and her younger son "went strange" and no one, including her husband and Ritsuka's teacher can stop it. At one point she ties him to a chair so she could go shopping, and it's very briefly mentioned she has her own Freudian Excuse too.
Ritsuko. But then, everyone in Neon Genesis Evangelion has so many Parental Issues it's not even funny. Asuka's the other big one for Mommy Issues; her mother rejected her after getting her soul ripped out and put in EVA-02 and believed that a doll was her daughter. After this had been going on for some time, she committed suicide... and Asuka found the body.
Shinji's Mother apparently put her soul into a Biomechanical Giant Robot created directly from the Angel that is also the Mother of Mankind. Shinji's reliance on his mother and his subsequent hatred of his father then springs from...ironically enough, his "angelic" mother. So both his parents are apparently off the deep end in terms of being half-way efficient in any given way, aside from traumatizing him into the justified breakdown he has at the end of End of Evangelion.
Although not his actual mother, Athena inflicted this training on young Hayate, shown in a flashback which included kicking him in the stomach while teaching him that he had to be financially able to care for a girl before he could have a girlfriend. Those lessons have still stuck with him to present (10 years later) and considering he's currently carrying a 150 million yen debt, he doesn't think he can be anyone's boyfriend. Ignoring, of course, that most of his Unwanted Harem could sit on their hands and make more in a day than he could if he spent the rest of his life working.
Hayate's actual mother and father are responsible for the 150 million yen debt and tried to sell him to the yakuza to pay it off. Hayate never seems bitter about this despite spending most of his life paying off his parent's debts and consistently getting stolen from (Hayate is only 16!).
His current debt is his own and self incurred. Mask the Money paid off the debt from his parents, in full.
Oskar von Reuentahl from Legend of Galactic Heroes is an interesting subversion in that he lacks the typical traits associated with the trope - he's not even a villain but a sort of Tragic Hero. He is, however, a bitter misogynist who never refuses women's advances but inevitably ends up breaking their heart when he gets bored of them. Later on he becomes involved in an unhealthy and abusive relationship with a woman whom he indirectly compares to his mother. The reason is his mother thinking his brown eye an omen about her brown-eyed lover and trying to gouge it out with a knife when he was just a baby. When she didn't succeed she went insane and eventually killed herself, driving Reuentahl's father to alcohol and emotional abuse.
The entirety of Brain Powerd. Every episode of it. In particular, Yuu and Johnathan.
Guts from Berserk. When he was growing up in a mercenary camp he lived for the approval and love of Gambino the leader of the mercenaries. Sadly, that love was not reciprocated since Gambino blamed Guts for the death of his lover Shisu (who rescued Guts as an infant) of plague, believing the boy to be bad luck. Gambino sold Guts to a pedophiliac soldier for three silver coins, then later tried to kill him after he got drunk. Guts killed him in self-defense, and ever since he had issues with being touched and had trouble forming emotional bonds. Guts was on the verge of getting over his Daddy Issues thanks to his time with the Hawks (Casca in particular), but then the Eclipse gave him even worse issues.
In the 2003 anime version of Fullmetal Alchemist, Envy is eventually revealed to be driven by daddy issues from his biological father, Hohenheim, abandoning him. On the flip side, his relationship with his mother Dante appears to be more cordial, despite her being the one who abuses, controls and manipulates him like a chess piece — of course, it's 'more cordial' in the sense that he only despises her to the level that she's not worth killing until after he's settled things with daddy and his half-brothers.
This is the reason why Minatsuki of Deadman Wonderland is so messed up. During the Great Tokyo Earthquake, her mother abandoned her in favor of rescuing a plant that had fallen down beside her.
Kanzaki from the Area 88 manga loved his late mother, but he was deeply traumatized by her suicide. Kanzaki's mother drove her car off a cliff (with Kanzaki inside) when he was a little boy, and the first thing he saw when he regained consciousness was his mother's dead body. We learn later in the manga that she was responsible for the deaths of Shin's parents, which motivates some of the things Kanzaki does to Shin.
Scarecrow, one of Batman's villains, was abused by his grandmother (father, in New 52) as a child. This isn't the sole reason why he became a psychotic who enjoyed instilling fear in others... but it certainly added to the problem.
Another Batman villain, Humpty Dumpty, was also abused by his grandmother. It was just one factor in a completely Crapsack childhood that drove him over the edge into insanity.
Rorschach from Watchmen had a mother who was an abusive prostitute, and this shaped his damaged psyche and negative attitude towards women to the point where he can't really function like a normal person.
You'd think Wolverine's son Daken would have Daddy Issues, but Word of God says otherwise. Daken's mother was killed before he was born (he was cut out of her body and survived only due to his inherited Healing Factor). It's very telling that as an award to himself for conquering the criminal underworld, Daken buys a painting depicting a baby suckling at the bare breast of its mother.
Reverse-Flash, in New 52, became a villain thanks to his Daddy Issues. He's actually Daniel West, Iris West's younger brother. Both of them were physically abused by their father, but Daniel took most of the heat because his father blamed him for his mother's death, since she died in childbirth. He eventually ran away from home and was cut off from the rest of the family, including the one person he loved, his sister; that also led him into the path that turned him into a small-time crook, arrested a mere days after attaining the age of majority. As soon as he got his Speed Force powers, he decided to go back in time and kill his father in order to fix his life.
Raoul Silva from Skyfall views his former superior, M, as a mother figure and his Start of Darkness was realizing that she had sold him out to the Chinese in exchange for the release of other agents. Hammered home when when he finally confronts M alone at the end of the movie and devolves into a whimpering child. Judging from Bond's reaction to M's death, he probably felt the same way about her.
The classic (cinematic) example is Norman Bates, the mother-fixated killer of Psycho.
Citizen Kane. While neither a sexual pervert nor a serial killer, one could argue that Kane's extreme hubris and mistreatment of women stem from him being unable to reconcile himself with his mother sending him away when he feels he did nothing wrong. His extreme materialism seems to be his way to telling himself that he deserves to be loved, when really, trying harder to reconcile with his mother before she died would have allowed him to live a much happier life without becoming a Manipulative Bastard.
Both Big Bads in the two Kung Fu Panda movies have been driven mainly by parental abandonment and being Well Done Son Guys. Not to let the bad guys get all the psychological issues, both Tigress and Po additionally have underlying issues involving their own parents too with both being orphans. This is to the point that a track for the score of the second movie is titled "Daddy Issues".
Subverted in Henry: Portrait of a Serial Killer. Henry tells of how he killed his abusive mother in self-defense, but he tells it in a bizarre, disjointed fashion, and occasionally forgets exactly how he killed her. It's then you realize that his terrible past is used to make him creepier, as you realize how disturbed and dangerous a person with such a past must have turned out to be.
Peter Foley, from the movie Copycat. He eventually killed his mom and set fire to her house.
Frank Zito from Maniac has severe mother issues, and he is compelled to decorate mannequins to look like her(using the scalps of women he murdered) and carries on conversations with them as if they were his mother.
The Aviator implies that this was one of the reasons (and there were a couple) that Howard Hughes had so many "eccentricities" in his adult life.
After the serial killing rapist in Gothika is unveiled, Dr. Grey speculates that the killer's accomplice grew up with an absent father and an over-dependent relationship with his mother which turned into sexual desire, got pleasure from torturing small animals as a kid, and is confused about his sexuality as an adult. Sherrif Ryan only disputes the part that he enjoyed killing animals.
Two of the lesser villains (meaning, those who aren't Hannibal Lecter) in Thomas Harris's series of thrillers have this background:
The childhood of Jame Gumb (from Silence of the Lambs) was never fully explained, but we do know that his mother was an absentee porn star.
Frances Dolarhyde (from Red Dragon) fairly takes the cake: raised by a sadistic grandmother who regularly threatened to castrate him for things as trivial as wetting the bed (he was around five years old at the time). In the 2002 movie version, Edward Norton's character even uses this as a Berserk Button to distract Dolarhyde during a fight.
The Red Rose Killer in Robert B. Parker's Crimson Joy, who killed women and left red roses at each scene, was abused by his mother, Rose Black.
John Dread, from Tad Williams's Otherland series, is a monster because his mother abused him while he was growing up. She specifically wanted her son to grow up to be a monster, and it worked. None of this makes him any less horrifying.
Ben Ladradun of Cold Fire was berated and abused by his mother for basically his entire life; he got respect and attention for the first time when he became a firefighting expert. And then promptly devolved into a pyromaniacSerial Killer by way of a Well-Intentioned Extremist when his methods caused such a drop in fires that people stopped listening to his advice to prepare for them. He also eventually murdered his mother in what is implied to be a fairly horrifying way.
In Death: Well, this trope has popped up a number of times! Just check out Glory In Death, Vengeance In Death, Visions In Death, Born In Death, and New York To Dallas.
All the Orkney boys in The Once and Future King are deeply affected by their twisted upbringing with Morgause: Gawain, though technically a good guy, is the only knight of the Round Table to have killed a woman in one of his uncontrollable rages; Agravaine is cruel and possessive to the point of killing their mother after he catches her sleeping with another, much younger knight, who he also kills; Gaheris has no mind and will of his own; Gareth takes it upon himself to resolve conflict and make everyone happy, even when they abuse him; and Mordred, though professing his deep hatred for their mother, begins adopting her attitude, habits, and mannerisms.
Emperor Ikurei Xerius from Second Apocalypse was incited by his mother to kill his father, and has an incestuous relationship with her going back to his childhood. As an adult, he is constantly torn between hating his mother and an intense sexual desire toward her.
Sylar from Heroes. His mother was completely obsessed with him being special... so it bled over into him and drove him nuts.
In Volume Three, Arthur and Angela exploit his Mommy Issues in order to get him to work for each of them. Naturally, when he finds out about this, let's just say "violent rage" is too broad to describe his reaction.
An episode of Law & Order: Special Victims Unit featured a mother who brainwashed her two sons to believe the world outside their apartment door was unspeakably hellish, and that being placed in a foster home was A Fate Worse Than Death. She mistreated them in other ways as well, and when it looked like they (surprise!) were going to be placed with foster parents, the older son killed his younger brother so he wouldn't have to experience those horrors(the gun jamming was the only thing keeping him from killing himself as well). Never mind that her eldest son had gone through foster care and was apparently normal, he was dead to her (literally - it was like a zombie was in the room).
Another episode featured a BTK-style killer whose mom had locked him in a closet while she went out to watch movies.
Still another features a woman who was accused of molesting a murdering one of her young, female piano students. She later confesses to the crime and tells the psychiatrist that her father molested her. Eventually it comes out that her mother had sexually abused her until well into her teens (and was still abusing her younger sister.)
The Law & Order: Criminal Intent episode "The Saint" featured Stephen Colbert (years before The Colbert Report, when he was still primarily a voice actor and The Daily Show correspondent) as a master forger who was trying to discredit a soon-to-be canonized priest because his mother used the guy's charity to literally steal his childhood — he had on average about a day to enjoy anything he bought or was given before his mother whisked it away, sold it, and gave the money to the charity. She actually calls him "ungrateful" to his face, when he finally breaks down and complains about his treatment at the end of the episode.
Another episode, "Diamond Dogs", features a heroin-addicted mother who intentionally hooked her own son on the drug, just so he'd always be dependent upon her and would assist her in the armed robberies that she undertook to support her own drug habit.
In The Sopranos, many of Tony's psychological problems can be traced back to a lifetime of manipulation and abuse inflicted on him by his mother, Livia, a woman with a borderline personality (or, to put it in ordinary language, a Manipulative Bitch). She even manipulates her brother-in-law Junior into putting a hit out on Tony.
The vampire Zachary Kralik definitely qualifies; he talked about his mother's abusing him, and he was obsessed enough to target Buffy's mother Joyce. Kralik (as mentioned in the page quote) killed and ate his mother before becoming a vampire.
"I have a problem with mothers. I'm aware of that."
Spike has been revealed to have mommy issues of a kind, in a story that involves incest but still makes both Spike and his mother sympathetic. Faith's mother (who spent her time "enjoying the drinking and passing out parts of life") isn't particularly squicky, so it's more of a straight Freudian Excuse than this trope; however, Faith taking Joyce hostage in This Year's Girl is clearly motivated by Mommy Issues.
Buffy had these with Joyce, because she had to keep the slayer thing secret. Then her mother becomes more supportive of her.
Jacob and the Man in Black's "Mother" (who isn't, really) on LOST. Her determination to keep the Man in Black from leaving the island causes him to dedicate his whole life (and well beyond) to doing just that.
Bree from Desperate Housewives is a bit two dimensional because of the creator basing her on his own mother.
The Cold Case episode "Blackout" featured a woman, who back in the days seduced her own 13-year old son. To make it even worse she later tried to do the same thing to her equally young grandson. Averted. The son grew into a decent man. It was her daughter who finally flipped and drowned the oedipal man-eater. And you can't blame her for it.
Another episode had two brothers whose mother was an abusive prostitute (no, they did not become vigilantes), and when one discovered that the other was with a prostitute... she was a friend and he was just trying to learn how to be sociable.
Lilly is menaced by a serial killer/rapist (I missed most of that arc) who believed he witnessed his abusive mother being raped when he was a child, but the truth is much worse his mother gave her son to the rapist to save herself.
An episode of CSI: Crime Scene Investigation featured a powerful man who was into roleplaying as an infant, even hiding a woman's baby so she'd provide him with breast milk. The woman tells the detectives that boss man-baby said he gave her baby to his mother, but that goes nowhere as said mother is hospitalized, has no knowledge of the baby or her estranged son, and is probably the least maternal person in Nevada (hence his need for all that maternal attention).
John Lennon, of The Beatles, was raised by his aunt Mimi and was just starting to know his birth mother Julia (who taught him how to play Buddy Holly's "That'll Be The Day" on the banjo, among other things, and which started or helped John into his career in music...either way: "Thank you, Julia!") when she was hit by a drunk-driving off-duty police officer; both his personal life and his professional/musical career were affected by this, with songs such as "Julia" (which is also about Yoko Ono) from the White Album, the heart-wrenching "Mother" from his first solo Plastic Ono Band album, and even naming his first son "Julian". He also attached on to Yoko specifically in this manner, referring to her as "Mother" (or "Madam") in "an off-hand way" (according to his final interview in Playboy).
Cyrano de Bergerac: In what is perhaps the most awesome subversion of this trope, Cyrano does not hate women, but he has a nose so big and ugly that he is utterly terrified of any women mocking him if they talk about love. The nose is only an excuse; his problems come from his childhood. His tragedy is that his Mommy Issues and his cultural views have ruined his life completely: He is a talented poet, duelist, soldier, philosopher, physicist, musician, playwright, and novelist who will never accomplish anything because of those traumas. The whole point of the play is that Cyrano could have won Roxane's (or any other woman's) heart any time he wanted, but he never did because of his self-loathing. (From a Certain Point of View, he is a serial killer, only he chases jerks). In the final act of the play, Cyrano, trying to comfort Roxane, lampshades this trope:
Cyrano:You blessed my life! Never on me had rested woman's love. My mother even could not find me fair: I had no sister; and, when grown a man, I feared the mistress who would mock at me. But I have had your friendship—grace to you A woman's charm has passed across my path.
In The Beauty Queen of Leenane by Martin McDonagh, Maureen has serious issues with her mother Mag. Mag is manipulative, emotionally abusive, passive aggressive, and selfish; Maureen is delusional, physically abusive, and eventually murders her mother. Charming pair.
Sephiroth from Final Fantasy VII. Oh so very much. You have to be "quite" messed up to want to try a smash a Meteor into the Planet so you could eat up all the Lifestream to become a God. Apparently, it's cause Mommy did that thousands of years before, and now he wants to be a good son and make her proud by doing the same!
Then there's the Remnants of Sephiroth in Advent Children. Keep in mind each of them is basically the Aspects of Sephiroth's Personality divided and eliminated of any direct influence from Jenova. They now mention "Mother" even MORE then Sephiroth himself....all THREE of them!
While not a villain, it's revealed in Metal Gear Solid 2 that Otacon had an incestuous relationship with his stepmother, which accounts for much of his social awkwardness and problems with intimacy.
Dragon Age: Morrigan's problems with her mother probably stem from being raised as a body for her mother to possess.
To a lesser degree in Dragon Age II, assuming you interpret Merrill (an orphan) and Merithari (her mentor who is certainly old enough to be her mother) this way.
Isaac in The Binding of Isaac spends a cutscene after each level crying to himself about the traumatic things his mother put him through, even before she started hearing the voice of God telling her to kill him.
Paranoiac has much more than Mommy Issues with Miki and her mother. Both are mentally ill, but Miki's mother is willing to support her depressed daughter nor was she will to support her mentally ill sister. Even when he daughter called and asked to come home after three nights of being chased by her dead aunt, she claims that her aunt's house is now her daughter's and to not come back.
This trope is Doctor XX's whole reason for supervillainy, though in her case its Daddy Issues.
Azula in Avatar: The Last Airbender . Interpretations of Ursa vary: the only time she appears, it's from Zuko's perspective of past events and, therefore, likely idealized and slightly unreliable. Azula, with her mind twisted by Ozai's emotionally abusive and violent tendencies, could only fixate on her belief that 'Mother loved Zuko best' and that 'my own mother thought I was a monster'. She points it out herself, but it's very clear she was always yearning for her mother's approval and love — and just as clear that Ursa was concerned for her. Fortunately, none of this is pertinent because the only thing you really need for Mommy Issues is the perception of an uncaring mother.
It seems like Azula's Mommy Issues have gotten even worse. Azula only recovered from her breakdown by believing that Ursa orchestrated a conspiracy to bring her down. The reason she's helping Zuko in his search is so she can kill Ursa.
Luanne's mother from King of the Hill was very abusive to her father causing him to flee, and is implied to have neglected her in the past. When she comes back she is okay as long as she doesn't have any alcohol; when she does she's borderline psychotic and will attack anyone who provokes her in the slightest. According to her, she views Luanne more as a sister than her daughter.
Grimes' mother on Ugly Americans pulls a Visual Pun (with being a literal mummy) definitely falls into this trope, as she doesn't approve of his (fake) demon girlfriend, Callie, and even tries to one-up her by showing how to reallykiss her little boy.
It's heavily implied that Dan from Dan Vs. has this.
Unfortunately, abusive or neglectful parenting situations do make it more likely that the child will have mental or behavior issues when they become adults, so this is Truth in Television.
Augusta Gein, mother of Ed Gein. It's questionable who was more unstable.
According to this, it is one of the top reasons for serial killing. Although often there is no reason, resulting in Reality Is Unrealistic since a Freudian Excuse reads more true in fiction than it actually is.
Implied with Adam Lanza, who murdered his mother in her sleep before snuffing out the lives of 26 others at Sandy Hook Elementary.
The reason Freud believed in this so strongly was because it actually applied to him. He really did have incestuous feelings for his mother. However, one critic pointed out a reason for this. Since Freud had a wet nurse, he instead recognized her as his "mother", and recognized his biological mother as just an attractive woman who cared very deeply for him.
Similarly, many Freud biographers say there is evidence he was sexually or at least physically abused by his father, meaning he has a, well, Freudian Excuse for both halves of the Oedipus Complex that's so bizarrely prominent in his theories.