Banjo and Kazooie themselves qualify in an unique way. Banjo has a blue backpack and wears yellow shorts while Kazooie is a red bird with some yellow feathers. Considering how important the team aspect is to the games, they end up fitting as this.
Mumbo Jumbo, who helps the duo out on several occasions, also qualify. He has a yellow skull-shaped head, large blue eyes, bright pink skin, and red feathers atop his head.
Billy Hatcher and the Giant Egg: Billy Hatcher's eyes, pants and gloves are blue, his neckerchief and comb are red, and his hair is blond (yellow).
Bladed Fury have you playing as a Warrior Princess out to save your kingdom, and you spend the whole game in a blue dress with flowing red ribbons.
Bob from Bubble Bobble series has blue skin, red hands and feet, and yellow spikes.
Cavern of Dreams: Fynn, the Delightful Dragon protagonist, has a red body with blue horns, wings, shoes, and a bandanna, as well as yellow spots on his face.
Chrono Trigger: Crono — Fiery red hair, a blue tunic, and a yellow kerchief ensures you won't lose sight of him. He's the hero, and for most of the game a required party member.
Cuphead and his brother Mugman are colored red and blue, respectively. The DLC introduces Ms. Chalice, who is yellow with a light blue skirt.
Double Subverted with Beppi the Clown. He has a red, white, and blue color scheme, but he's a boss in the game who made a Deal with the Devil as some point. The double subversion comes with the Golden Ending, which implies that he — and most of the other bosses — aren't actually malicious.
Helena is the deuteragonist of the DOA series. She has blonde hair and has worn blue or red opera outfits.
Tina Armstrong also has blonde hair and her most recurring outfit is an American Flag Bikini.
Nero, the main protagonist of Devil May Cry 4, wears a blue coat with red inner lining and a red hoodie underneath. His Devil Bringer has red scales and blue flesh. In Devil May Cry 5, he wears a dark blue hooded jacket and dark crimson shirt. His outfit colors reflect how he is a combination of Dante and Vergil who wear red and blue respectively.
Dillon's Rolling Western: Dillon, the old west hero and titular character, is a yellow armadillo with a bright red shell and blue scarf. The scarf has some thin yellow patterns on it, too.
In Eschatos, while the color of the player's ship can be customized, it defaults to red.
In the Fatal Fury series, main hero Terry Bogard's iconic outfit is a red and white baseball cap, a red sleeveless jacket, white T-shirt, blue jeans and red sneakers.
Almost every Fire Emblem Lord wears this color scheme too. Usually blue clothes with a yellow trim, and a red cape (at least on the inside of it). Marth kickstarted the trend, followed by Seliph, all four ElibeLords.Ike sported this color scheme as the Hero of Tellius, despite not being a noble like previous heroes. Micaiah wears it as well in much subtler fashion. Chrom only wears desaturated and darker blue clothes with a yellow trim, however his usual sword and its scabbard are red. In addition to being the main characters, they also cause an instant game over if they die, so it's important to watch them on the map.
Captain Falcon of F-Zero — blue body suit, red helmet, yellow boots and nipples. Despite having a very loose plot, he's the series' most iconic character, default choice for player one, and the Smash Bros. representative. The anime adaptation makes it that 'Captain Falcon' is a mantle, not an individual, making the color scheme even more relevant.
Despite Venus adepts association with the color yellow, Isaac the hero of Golden Sun wears a blue outift with a red breast plate. The only yellow on him are his Scarf of Asskicking and blonde hair.
His son Matthew in Golden Sun: Dark Dawn wears a blue jacket, red shirt, and a scarf so similar to Isaac's that fans often say it is the same one.
In KanColle, we have Iowa. Being an American battleship, she has reds and blues throughout her costume and riggings.
The King of Fighters: Inverted with one of The King of Fighters XV's newcomers, Krohnen. Despite his red scarf and goggles, blue hair and glove, and yellow biker jacket, he's an anti-social jackass, kidnapper of a minor (albeit said minor ran off from her guardians for a very petty reason), and years ago, attempted murderer.
Kingdom Hearts: Being a Mickey Mouse stand-in, Sora's costumes are primarily red, yellow, and black. However to invoke this trope as the hero, he does have bright blue eyes, a blue stripe near the hilt of his sword and subtle blue accents on most of his costumes. Usually the belt, hood, or undershirt.
The titular hero is a pink creature with red shoes and blue eyes. Additionally, he is often seen alongside a yellow warp star that serves as his main mode of transportation.
King Dedede, while originally Kirby’s archenemy, has become more of a protagonist as the series has progressed. He is a blue bird with a yellow beak, and his outfit includes a red coat and hat, yellow gloves and shoes (and sometimes a yellow undershirt), and a sash in various primary colours.
Meta Knight is a Downplayed example. He has purple hues in his design to indicate his status as a gruff, hardened badass. However, he also has blue skin, yellow eyes and a gilded sword, showcasing his noble character that occasionally helps out Kirby on his adventures.
The eponymous character of the Klonoa series always wears clothing that is prominently blue, red, and yellow. Two features of his outfit that remain the most consistent across his appearances are that his hat is blue and that he wears a pair of yellow cartoon gloves.
Kuru Kuru Kururin: Kururin is the series protagonist and has blue feathers, a yellow beak and legs, and a red scarf and goggles respectively.
The Legend of Tian-ding has the titular protagonist, a Just Like Robin Hood hero who battles corrupt landowners and ruthless dictators for the civilians, and spends the entire game wearing blue with a flowing red sash.
Although Link is typically associated with green, his iconic Hylian Shield has a red bird and yellow Triforce against a blue field.
Link and Ganondorf make an interesting double subversion of the trope. Link is (mostly) dressed in green, and Ganondorf in red and gold, which is the original subversion. However, Link's outfit has white accents, while Ganondorf's has black ones. Also, as exampled above, Link's shield has primary colors, and in The Legend of Zelda: Ocarina of Time he wears a red belt. Ganondorf on the other hand frequently uses purple magic blasts, and have deep green skin.
Princess Zelda, the namesake of the series, plays this straight with her disguises. Sheik not only has blonde hair, but wears blue and white clothing with a red Shiekah eye on the chest. Tetra is also blonde and wears a blue vest with a red kerchief and belt.
The Legend of Zelda: Breath of the Wild changes it up by having Link wear a blue tunic instead of his traditional green one since blue is a sign of royalty in the game's story, which makes sense since he was Zelda's personal knight/bodyguard. The green tunic can be obtained however. The Hylian Shield is also hidden and it still retains its traditional colors.
Invoked and inverted in The Legend of Zelda: A Link to the Past. Agahnim saved Hyrule from disasters with his magic, and he wears a red cloak with a blue Shiekah eye and gold details. However, he used the trust he gained from his "good deeds" to usurp the throne of Hyrule and break the seal leading to the Dark World to free Ganon, his original self.
Mega Man is usually just blue, but some incarnations will give him red and yellow accents. MegaMan.exe and Geo Stelar are the straightest examples.
Mega Man X is blue with red accents by default, but in his higher level armors he gains plenty of yellow trims as well. As he becomes more heroic he embodies the trope even more.
Zero in the Mega Man Zero series wears a dark blue jumpsuit coupled with his iconic red armor and blond hair.
Originally averted in Metroid as Samus' armor is red, orange and yellow with green accents. However when they finally codified her under armor Zero Suit, it's blue, with a pink design on the back and red scrunchie, and offset by her long yellow blonde hair. Under her hard exterior is an iconic hero.
Monster Hunter Generations features this with two of the Four Mascots of the game: Glavenus and Gammoth. The former is the monster described as The Leader of the Elite Four (ie: The Hero) is a primarily red Brute Wyvern, with blue highlights and a yellow underbelly; The latter is a massive mammoth-like fanged beast with fur covering its huge body that is mostly bluish, with white and red on its trunk, legs, back and underside.
All three of the Mother main protagonists wear this color scheme. Ninten and Ness, the first two heroes, wear nearly identical clothes. A red and blue baseball cap, and a blue and yellow striped shirt, among other elements.
It's played with Lucas and Claus. Claus wears the iconic blue and yellow striped shirt, and has bright red hair instead of a cap. He's much more heroic and extroverted, which leads to his downfall. This leaves Lucas, the more timid brother, to grow into the main hero. He wears a red and yellow shirt and blue jeans, invoking the trope in a different way than the heroes before him.
Lucas' partners, Kumatora and Duster, both feature blue and red in their designs as well.
Onechanbara has Aya and Saki before the Z series. Aya wears a (feminine) red bikini, yellow-tan cowboy hat with a blue draw string, yellow tan boots, and a blue sheath for one of her swords. Saki wears a blue Sailor Fuku uniform with a red bow and white sleeve and collar trimmings/accents. During the Z series, both traded their outfits in for Paint It Black and Elegant Gothic Lolita fashion respectively. Kagura has a similar color motif to what Aya used to wear, and in addition has eyes that are blue.
The main character of the Pac-Man series has yellow skin and red boots, and in some outings (most notably his GhostlyAdventures incarnation) blue eyes.
Captain Olimar from Pikmin has a yellow spacesuit with red accents. In the third game, he even has two blue buttons on his suit. This trope is even further supported by the red, yellow and blue Pikmin types he has been assisted by since the series' beginning.
Olimar's companion Louie has a similar spacesuit, but with blue accents instead of red.
The enemies in the series don't have any special color scheme, showing how the world in the game works as an ecosystem rather than a world about good and evil. However, the Emperor Bulblax is green-coloured with an (in)famous purple tongue, and being the final boss from the first game, it is widely considered by fans to be Olimar's archenemy.
Pokémon protagonists tend to feature primary colors with blacks and whites in their wardrobes. Some of the female ones replace red with pink. In further contrast, villains favor black, white, and grey (except for Team Flare, who almost all wear eye-searingly bright red).
In Pokémon Black 2 and White 2, the player can act in movies, including a superhero series. In these movies, the player is cast as the hero and is dressed up in bright primary colors; while Brycen, as the villainous Brycen-Man, wears purple with green accents.
In Polyroll, the titular hero is a red pill bug with a blue shell.
In Puyo Puyo, Amitie's clothing is almost always a variation of red/pink, blue, and yellow. The sole exception is a green bracelet on her arm.
Shyna from Silhouette Mirage wears a half-red half-blue get-up that looks kind of similar to what a witch would wear, minus the wings on her hat. Plus she's a blonde, so that's the yellow part down. This is actually important, since in her game every living thing is either "Silhouette"(blue) or "Mirage"(red). Her having both so prominently in her outfit emphasizes her status as a Yin-Yang Bomb in the world.
The titular character of Sly Cooper is a grey-furred raccoon who wears a predominantly blue outfit with yellow accents, along with a red backpack or leg pouch. Likewise, his friend Murray— a superhero fan himself— is a pink hippo Bruiser with a Soft Center who wears a blue shirt and scarf, along with a red mask and fingerless gloves.
Both Ryu and Ken, especially the latter with his red gi, blonde hair and blue Hadoukens. Ryu has his red bandanna and gloves plus the same blue Hadoukens, but no yellow. This is relevant as Ryu tends to flirt with his Dark Side every now and then whereas Ken doesn't have this problem.
Chun-Li tends to wear blue and yellow/gold outfits, depending on the game and timeline.
Three of the franchise's Shotoclone characters would qualify. First there is Sakura, Ryu's Ascended Fangirl who wears a white and blue school uniform and red sneakers and sparring gloves. Her friend and rival Karin has blonde hair and wears a red school uniform and a blue hair ribbon. Sean Matsuda, Ken's protege, wears a yellow gi and red sparring gloves. In Street Fighter V, he wears a yellow jogging outfit with red sneakers and his signature red gloves.
Rainbow Mika has blonde hair and wears a blue mask and outfit.
Street Fighter III has Alex, Elena, Oro, Dudley, and Makoto. Alex is blonde, wears a red bandana with red gloves, and green cargo pants. He's the main protagonist of this game. Elena wears a white bikini, is blue eyed, wears ringed necklaces, brackets, thigh, leg, and ankle bracelets with all three primary colors. Oro has yellow skin, has glowing red eyes, and wears red. Dudley wears blue boxing gloves and has blue eyes, while wearing a white undershirt with green trousers. Makoto wears a white karate gi, has a red shirt/sports bra underneath, and has a long yellow scarf around her neck.
There are exceptions:
Inverted with the three main members of the villainous Shadaloo organization: M. Bison, Balrog, and Vega. They all wear red and blue, with varying degrees of yellow as well (depending on the series' entry). In Bison's case, the blue on his clothes has become darker as the series went on, almost making him Red and Black and Evil All Over.
Subverted with Gill in III, who is a Well-Intentioned ExtremistAnti-Villain. He wears a white thong, has long blonde hair, has skin painted vertically with red on his right side half, and blue on his left side half. Gill is the master of elemental techniques, Fire and Ice.
Cammy White has blonde hair and wears a green Leotard of Power with a red cap and red gloves. Her leotard is colored blue in her "Killer Bee" persona when she was a villain which could count as a subversion of this trope.
The protagonists in the Streets of Rage series all have the primary colors in some fashion. Axel wears a white shirt with blue jeans, a blue headband, red gloves, his shoes being white and red, and his hair is yellow. Blaze wears nothing but a red top, red skirt, and red shoes. Adam wears black pants with a yellow shirt. Skate wears yellow shirt, white shorts, red roller-skates, and a red baseball cap. Max wears blue tights with yellow thunderbolts and his boots are red. Dr. Zan has red shoe and his torso is blue. Cherry, being the daughter of Adam, also wears a yellow shirt, blue jeans, and has dyed red hair.
Super Mario Bros.: Super Mario — blue overalls, red shirt and hat, yellow buttons. He was designed as the hero of Donkey Kong after Shigeru Miyamoto lost the rights to use Popeye. Since then, he's gone on to become the most iconic hero, and character period, in gaming. Essentially the Superman of his medium.
Princess Peach wears a pink dress, blue jewelry and has blonde hair. Likewise, Toad's most common outfit consists of a blue vest with yellow outlines and red-spotted mushroom cap.
One of the trailers for Super Smash Bros. makes a point to compare four big mascots in terms of their primary colors: Mario representing Red, Sonic and Mega Man each representing Blue, and the newly-revealed Pac-Man representing Yellow.
In Undertale, Undyne, considered the underground's greatest hero, has blue skin, red hair, and yellow eyes.
Furthermore, throughout the game, the protagonist wears a blue and magenta striped shirt. If you get the "genocide" (bad) ending, it reveals that the 'Fallen Child' looks nearly identical to the protagonist, but wears a yellow and mint green shirt of similar design.
Virtua Fighter: Sarah Bryant has blonde hair and wears a blue bodysuit.
