Ami Kawashima from Toradora!. She started as a Bitch in Sheep's Clothing, but eventually learned to be a somehow more balanced snarky Jerk with a Heart of Gold. Justified in that, at first, almost everyone thinks Ami is a bitch (except Kitamura, a close friend of hers). It is later revealed she has to deal with creepy stalkers and legions of fans almost every day, due to being a famous teen model.
Emily Sevensheep from Mahou Sensei Negima!. Which makes her death in Yue's arms as heartbreaking as possible, and her subsequent resurrection (along with countless others) courtesy of Negi and Asuna's restoration of Mundus Magicus' denizens all the more heartwarming.
Ino Yamanaka from Naruto is a milder version. Though her base Alpha Bitchiness is debatable: she diets, shops, etc, but also fights villains and learns killer techniques on regular basis, which most Alpha Bitches don't do, as a young girl, she was the one to reach out to bullied Shrinking Violet Sakura by teaching her how to accentuate her apparently large forehead, introduce her to her friends, and stick up for her when an actual Alpha Bitch Ami and her Girl Posse were trying to pick a fight.
Fatina from The Tower of Druaga definitely feels like one of these. She's materialistic, vain (her whole reason for adventuring is to become rich so that she can buy her favorite fashion accessories), has a tendency to be judgmental and slap labels on and look down on people, enjoys mild bullying... is highly concerned about her companions, and has a strong sense of duty. When Jil is depressed after the events of season 1, Fatina is the one who takes care of him and works hard supporting him financially for several months.
If One Piece had taken place in a high school, then Boa Hancock would be one of these. She takes care of her people and is brave and caring when it comes to her sisters and those her earn her favor, and has a genuinely good Freudian Excuse. But to everyone else well… To take a direct quote from her:
"Whether I kick a kitten... Tear off your ears... Even slaughter innocent people... The world will never cease to forgive my actions! Why, you ask? Why, it is because I am beautiful!"
Sheryl Nome from Macross Frontier. Sure, she can steal Alto's free day just for fun and bend everybody to her schedule, but she is generally sweet and, friendly, and actually helps people around her.
Izumo Kamiki from Blue Exorcist is an Ice Queen, but not only is she slowly defrosting, she is the first to accept the fact that Rin is the son of Satan. In her own way. Interestingly, her back-story suggests that she isn't exactly popular (due to her ability to see demons) and only has one friend, which she insists is all she needs.
Yano from Kimi ni Todoke is not someone you want to get on the bad side of, but you have to really deserve it to get there. Otherwise, she's actually very friendly, even for this trope.
Kurumi becomes this throughout the series as well.
Saki Tenjouin in To Love-Ru. She comes off as a queen bee (even proudly declaring herself the queen of the school at every opportunity), but when someone needs help she is not hesitant to do what she can.
Alice from Ikoku Meiro no Croisée can't help but showing her exuberant young-girl side, despite her desire to be seen as a classy rich lady.
Sumire Shouda from Gakuen Alice is this type. Throughout the series she is the bossiest and snobbiest girl in the class, holds Alices well above non-Alices and bullies Mikan when she first arrives at the Academy. However, she becomes helpful and resourceful and even kind when there is trouble and helps organise the students to fight. In later chapters she always takes Mikan's side when she is in trouble.
Sena Kashiwazaki of Boku wa Tomodachi ga Sukunai is a ridiculously hotRich Bitch who lords herself over her schoolmates at the academy her father runs. Then she signs up for the Neighbors Club and reveals that she wanted true friends. Thus she does make some within the club in the form of Kodaka Hasegawa, a British-Japanese boy whose blonde hair and oriental face make his classmates mistake him for a "delinquent" and, secretly, Club President Yozora Mikazuki (whose Jerkass tendencies hide her social-relationship problems as grave, if not even worse, than Sena's).
Touka Ryuumonbuchi from Saki. She's a total bitch to everyone who isn't from Ryuumonbuchi High School (yes, the school belongs to her family), but is seriously nurturing toward everyone whom she takes under her wings, especially the Killer Rabbit Koromo.
Kourogi Mikage from Nononono who is a gold medalist and having both looks and brains is thought of (and thinks of herself) as a national celebrity. At first glance she is a grade A Alpha Bitch that treats others as inferior to her and is ready to make their life miserable if they dare to deny her anything, once you get to know her though it turns out that despite all her arrogance she is a decent and caring person whose bithiness comes as much from her "upper class" status as from her inability to honestly express her feelings.
One-time character Sonoko Iijyuin from Sailor Moon Stars. Grade A Alpha Bitch to Usagi, demanding her to leave Seiya alone since she's his number 1 fan and challenging her to beat her at her sport... which is a totally inequal position, as Usa is a Cute Clumsy Girl while Sonoko is a Passionate Sports Girl and REALLY good at softball. But when she sees that Usagi is still determined to try it, she softens up and sees Usagi as a Worthy Opponent. And THEN, she's attacked by Lead Crow and forcibly turned into a monster - but Usagi, as Sailor Moon, manages to save her.
Marianne Hamilton from Ashita no Nadja. Very rich, very blunt, a Clingy Jealous Girl. Loves her dude Francis sincerely despite her clinginess, aids Nadja in her ultimate quest, quietly and tearfully walks away when she sees that Francis has chosen Nadja in the end.
"Monkey Queen"/Reika Jogasaki from Switch Girl. In the early volumes, she does everything to ruin Nika's life, setting up traps and malefic plans. But as the story goes, she reveals herself to be a nice, kind-hearted person, as she supports and hels Nika, especially during the Shutei arc.
Akina in Shinozakisan Ki Wo Ota Shika Ni would like to be an Alpha Bitch but missed her chance after being sick for a week, so nows she's forced to be friends with Otaku, but whats worse is not only is she starting to fall for an Otaku, she's strating to become one herself.
Cornelia from W.I.T.C.H. was known to be incredibly disagreeable after getting her powers, but eventually gets used to it. She's also the local Bully Hunter, being the one who protects younger and/or new students from the local bullies (that's how she first met Taranee) and keeps in line the actual Alpha Bitches.
Emma Frost from X-Men. She's almost always conceited, extremely critical, and absolutely ruthless in any kind of fight. Not to mention she intentionally wears all those skimpy outfits just to get attention. However, she's a Mama Bear to anyone who's officially or unofficially her student, and she's almost always been a loyal, reliable member of the various teams she's belonged to.
Guillotine from Minimonsters is a good example. She's a goth girl who bullies the Frank's gang alongside (or not) his "boyfriend" Morty (The leader of the gang and real Alpha Bitch, although is male). In spite of that, she's best friends with Piruja (one of the Frank's gang) and helps her to conquer Victor (The spoiled protagonist), although she absolutely doesn't get along with him and his friends.
Gen from Ice Princess starts out a full-fledged Alpha Bitch, but eventually becomes Casey's advocate and guide in the ice-skating world.
Jessica Spencer of The Hot Chick is a Jerkass to certain people she doesn't like, but takes good care of her baby brother. The Pet the Dog moment with her brother is important because it makes it easy for us to feel sorry for her later on when she is magically transformed into a man (don't ask).
Claire from The Breakfast Club. In fact, her bitchiness comes less from herself and more from peer pressure, and it's shown that deep down she's miserable due to it.
Deconstructed in The Hole with Keira Knightley's character Frankie. When Liz tells her story to the police we see in flashbacks that Frankie is popular but isn't bitchy to Liz and helps her out (it's implied that Liz does her homework for her). Then we learn that Liz's story is a lie and we see real flashbacks and Frankie fits the Alpha Bitch stereotype down to a T. Though Liz is actually worse than her.
Dylan Schoenfield of Geek Charming (both the film and the book it's based on) could be a codifier for this trope.
Amanda Jones of Some Kind of Wonderful is set up to be this, but really isn't. In fact both her nastiness and her social status stem from her Manipulative Bastard boyfriend, Hardy Jenns, and once they breakup she improves very quickly.
Mikaela Banes from Transformers looks like she's developing into this, before the plot kicks into high gear and her troubled history comes out.
Ashley and Ashlyn from Final Destination 3, despite behaving like typical ditzy popular girls, are actually friendly towards the protagonist Wendy. In their funeral, Ian mentions how they had never done anything bad to anybody.
Jules from The Cabin in the Woods is an interesting subversion of the trope...as is every other trope in this movie. She's the typical alpha bitch sex tease, but only because of the pheromones and chemicals she's been given by the white collars, to change her behavior and intelligence. In truth, she's very friendly, loveable and funny, as seen in the beginning of the film.
Misa from Oyayubihime is nosy, rude and gossipy. But she definitely isn't a bully, and she stands up to Saeko in spite of being blackmailed into staying quiet. Not to mention, her fights with the teacher provide much comic relief.
GBF focuses on a high school with three alpha bitches, all of whom reveal a far nicer side. 'Shley is willing to befriend Tanner despite Mormonism forbidding it, and is generally the nicest and most approachable out of the three of them. Fawcett is the only one to stand up for Tanner re: the school's homophobic prom policies. Caprice is the only girl to understand Tanner needs a romantic life and isn't a neutered purse-poodle- so she tries to set him up with a hot British guy.
Lana in The Princess Diaries. By the end of the series, she's become close friends with Mia and is shown to be genuinely sympathetic.
The protagonist of Daughter Of The Drow. Liriel was a minor member of the ruling clan popular among young party-loving nobles, and wasn't more malevolent than being good at the Drow brand of humour required. Later in the Academy she habitually pranked her peers, mainly the plump girl she referred to as "a peasant" (in fact, noble, but from an agriculture-focused House) — a senior student known as humourless and too vicious with younger students. Which only made the perpetrator more popular as a wizard sneaky enough to repeatedly humiliate the hated jerk without leaving any proof.
Constanza Grayfoot in the Midnighters series by Scott Westerfeld may not be particularly nice to any of the other Midnighters - though she will admit that Dess 'knows her trig' - but she's a genuine and supportive friend to Jess, though a somewhat superficial one.
Ginevra Fanshawe in Charlotte Brontë's Villette. She is completely open about being a superficial Gold Digger, but she seems to genuinely value Lucy's friendship.
Fleur Delacour of Beauxbatons Academy in the Harry Potter books gets a lot of flack for dating Bill Weasley, due to his family believing her to be a pure Alpha Bitch who's only superficially interested in him. She proves them wrong by standing by her man, even after his face becomes mauled. Though part of her reasoning is in pure Alpha Bitch fashion - that she's beautiful enough for the both of them, and that the scars Bill received from Greyback prove that her husband is brave. She then promptly starts cleaning his wounds.
There's also Cho Chang of Ravenclaw, who's pretty, popular, a star Quidditch player, has her own Girl Posse, but is actually a Nice Girl who just has some severe emotional and psychological problems. Her first boyfriend being casually murdered by the Big Bad didn't help.
The Twilight series has Rosalie Hale for the vampires and Leah Clearwater for the werewolves.
Bethany Davis in Every Other Day by Jennifer Lynn Barnes. Lampshaded:
At Degrassi, both Paige (S1-S5) and Holly J (S7-S11) start out as the standard Alpha Bitches, but due to Character Development Paige comes to the point where she's ready to stop worrying about what other people think and have a lesbian relationship with Alex in her senior year. Holly J also grows into this trope by the time she's a senior.
Caroline from The Vampire Diaries. Blonde, popular, pretty, ditzy (not helped by having been repeatedly mind controlled), but nice enough.
Quinn Fabray starts off as a nasty Alpha Bitch, gets pregnant and becomes a Fallen Princess. Now that she's had the baby she's back to being The Cheerleader... but is still friends with everyone in the glee club. Except Rachel. Unfortunately, it seems her character has reverted back to her original personality. See this chart for a general outline of her inconsistent personality throughout the first half of season two.
Santana Lopez started out as The Dragon to Quinn's Alpha Bitch only to inherit the top title when Quinn became the Fallen Princess. She's now nursing a healthy dose of Gayngst. Also, she's been getting more and more sweet moments, with Brittany in particular and arguably the club in general. All while keeping her spiciness.
Glee seems to be unable to function without at least one of these in the cast. The newest version is new head cheerleader Kitty, who spends most of a season in the New Directions apparently just to mess with them. Then, when she hears of other popular girls harassing Unique, she vehemently demands their names, so she can put Nair in their shampoo bottles. Off the rest of the cast's shocked looks, she finally admits that they're her friends... and naturally, she will deny that at the top of her lungs outside of that room.
Lexi of A.N.T. Farm started the show a straight-up Alpha Bitch, but has slowly been shaping up as this, getting some moments of potential friendship with Chyna and even some Ship Tease with Chyna's brother, Cameron.
Maria Joaquina from Carrusel. She had two Kick the Dog moments at the beginning, when she ripped the card that Cirilo gave her for her birthday and then when she ratted Marcelina for cheating on a test. The second one, however, bit her in the butt badly as her classmates (Cirilo included) isolated her; Maria Joaquina ended up breaking downin tears due to this, and after that she became the Lovable Alpha Bitch we know and love.
Rachel on Friends started off like this before Character Development. This goes back to her days in high school when she was a spoiled Alpha Bitch cheerleader but was still friends with the unpopular Monica.
Examples of this abound on America's Next Top Model. Bianca from Cycle 9 was a monster, picking on poor Aspie Heather and Stripper With A Heart Of Gold Lisa. But you can't hate her too much when her disses are as poetic as "check your thighs in the mirror, and I'm done" and her claim that she's a "fun bitch" not a "bitchy bitch". It's more fun to judge America's Next Top Model contestants by their capacity for Memetic Mutation as opposed to their actual modelling ability.
Lydia Martin from Teen Wolf, especially when she's around Allison or Jackson. But she's a hard character to hate once you've seen her season-long descent into hallucination-induced insanity
Mira Kagami in Tokimeki Memorial 1 when you get to see her Hidden Depths (dead father, painful rejections, poverty). Accentuated in the various tie-in Radio Drama, OVA, and spin-off games, which flesh out her character further.
Etoile, in Rhapsody: A Musical Adventure, is set up initially as the Alpha Bitch, but you mostly see her nicer side during your interactions with her in the game.
To a degree, Princess L'Arachel from Fire Emblem: The Sacred Stones. She's shown to be selfish, kinda childish, and very bombastic, but she's also very brave and kindhearted when push comes to shove, like when she manages to pull Eirika out of an Heroic BSOD after losing the Stone of Renais to Lyon and gives her very valuable advice.
Clarine from Fire Emblem: Sword of Seals. She keeps demanding vassalage from Rutger and Lance and can be pretty mean to those who get close to her brother Klein, but she also helps Dorothy with her self-esteem without any second intentions and secretly fears that, once the "adventure" is over, she won't be able to see the outside world again.
Yukari of Persona 3. She's a popular Tsundere on campus, and comes off as cheery, but also quite snarky on a bad day. Annoying as she seems, it's appropriate to call her a Jerk Ass Woobie rather than straight up Jerk Ass due to her very troubled backstory.
GLaDOS of Portal is one of the most loved video game characters, but she is horrible and verbally abusive toward the player character all the time. Despite this, as the sequel shows, she's not all bad at, er, "heart". At least until she deletes Caroline. Considering her history, though, that might be another lie.
Mandy in Bully first appears to be the epitome of Alpha Bitchdom (beautiful, head cheerleader, dates the captain of the school football team, is viciously cruel to the nerd girl etc.) however the inevitable humiliation she receives is not actually Played for Laughs when we see her reaction to it, and she is also shown to be well aware of how horrible she is and that it stems from her own insecurities.
Sasasegawa Sasami from Little Busters! is beautiful, popular, smart, and the captain and star player of the girls' softball team. She also has minions who follow her everywhere and a great tendency for gloating. She also happens to genuinely respect Rin as her rival, considers it important to take responsibility for the negative actions of her underclassmen, and even ends up joining the Little Busters to fill in for Rin in her route.
Penny of Penny and Aggie appears at the beginning of the comic to be a straight-up Alpha Bitch, and indeed Aggie and certain other characters see her that way for much of the series. However, while Penny is materialistic and often snobby, she's also genuinely ethical and compassionate. She even admits to Aggie, when they bury the hatchet and become friends, that "I don't really need the perfect shoes. It's just fun to pretend I do."
Chrys'tel Vel'Sharen of Drowtales starts the series as a straight Alpha Bitch, but she's quickly shown to defend her roommate Faen from being tormented by the other girls. Later on she begins to question what's going on in her own family and actually becomes The Mole to her aunt.
Zulenna in Girl Genius at first was a complete Spoiled Brat who looked down at Agatha (but wasn't that popular). When it was revealed that Agatha was an Heterodyne, Zulenna paid her as much respect as she despised her earlier. And even gave her life to slow the soldiers pursuing Agatha.
In Eerie Cuties, this'd be Layla Delacroix. She's the most popular girl at Charybdis Heights and she's hot enough that Even the Girls Want Her. But she's still regarded as an Ice Queen, by some of the students, due to her aloofness and her snarky nature. Yet, Layla's been shown to be fairly responsibile and even helps organize activities at the school, as seen in the "Kissing Booth" bonus story in the print edition of vol.1. Nor is she the type to hold grudges... unless the other girl's name is MelissaHellrune.
Aki of Sailor Nothing has shades of this. Even before her Break the Haughty chapter, she is (secretly) friends with Himei, the class loser. She later considers her "breaking" to be the best thing that ever happened to her, as it freed her from the shallow pursuit of popularity.
Worm sounds a lot like this trope though it never plays it outright. Tattletale is explicitly beautiful and has manipulation as a superpower. However despite her very bitchy tendencies towards the world at large she lacks any crowd to be in with and is a loyal friend to Taylor from their first meeting. What little is known of her backstory would suggest that she probably used to be this played straight, given her honest concern about her brother and beating herself up for not seeing the signs of his impending suicide. She certainly became this, given how she ran away when her father attempting to use her power for incredibly selfish ends.
Rhonda Wellington Lloyd from Hey Arnold!. Despite engaging in typical Alpha Bitch activities, she can be remarkably friendly. Her best friend is a down-to-Earth bug collector, she has a great capacity for sympathy to those less fortunate, plays sports with the gang all the time, and doesn't hold a grudge against the guy who stalked and blackmailed her into dating him for a week.
Lo from Stoked technically should be the Alpha Bitch, given her "pedigree". She's a spoiled, gorgeous, manipulative, rich girl with a spray-on tan...however, she's also friendly and loyal, downright sweet even, and loves her friends.
Sissi of Code Lyoko, especially in Seasons 2 and 4 when there were a lot more episodes with her written that way, though she had a few moments in the first season as well. Much of her setbacks to being a just plain Alpha Bitch were do to the literal Reset Button the show likes to use, and being a just plain Alpha Bitch to start with was because of a stupid misunderstanding between the heroes and her back in the prequel episodes. In the series finale, her status as Lovable Alpha Bitch finally sticks when the heroes make her a part of their group.
Courtney Gripling from As Told by Ginger. She may have a somewhat...anthropological approach to the world outside her sphere, but she really does have a kind heart. Her best friend Miranda Kilgallen is closer to the more typical Alpha Bitch but even she softens as the series goes on.
Brittany Taylor and the other cheerleaders have shades of this. Her boyfriend Kevin Thompson is also a male version, averting most of the expected Jerk Jock attributes. Kevin (And the cheerleaders to a lesser extent) still tend to be jerks to Daria and Jane, but that's more due to their complete inability to understand people different than them, rather than any kind of malice. They simply don't know when they're being rude.
Cassandra in Sabrina's Secret Life. She started as the witchy replacement of Alpha Bitch Gem Stone. But, as the series progresses, she becames more kind-hearted and, at the end, she and Sabrina officially are good friends.
Liz from The Spectacular Spider-Man becomes this via Character Development, going from stuck-up in the second episode to eventually dating dorky Peter. Mary Jane also may count, as she interacts easily with both the popular and geeky kids, while Glory also has at least some hints of this, quickly bonding with Harry for a time.
Stephanie Knightleigh in Edgar & Ellen occasionally falls into this, either being nice toward her little brother, helpful toward her equally jerkish advesaries, or being surpisingly Badass in her scuffles with them that even they respect her for it. This is a contrast to the book series the show is loosely based on, where the twins gradually become better people while Stephanie is a sociopath with little in the way of redeeming traits.
Clover from Totally Spies!, in contrast to Mandy who was more of a classic Alpha Bitch. While Clover can be kind of rude, snobby and conceited, she understands the importance of friendship and teamwork, unlike Mandy.
However, Mandy has been shown to have a nicer side to her personality, but unfortunately, it never lasts long and she pretty much always goes back to being mean again if she's provoked in some way.
Angelica Pickles from All Grown Up!, especially when compared to straight-up Alpha Bitch Savannah.
Ashley A from Recess could count. When she is kicked out of the clique she befriends Gretchen and during the Little Miss Blush beauty pageant she secretly congratulates Spinelli. She has also asked the gang for help on other occasions, and is seen talking to the less popular kids on the playground like The Diggers. Sometimes the other three Ashleys can also be convinced to be nice and do good, like in "The Great Can Drive" and "League of Randalls".