Mukokuseki is the use of ambiguous racial features in anime, with characters having traits like wide eyes, light skin, great stature, and various hair colors. It literally means "stateless" (i.e. "without nationality"), though the term relates to more abstract anime and is used for hyperbole in this case.
Note that just because you perceive someone as being a particular ethnicity despite Word Of God saying otherwise doesn't mean it is this trope. The trope appears when characters of the same race look completely different, or characters of different races look essentially the same. It's the ambiguity that arises when there is a lack of Facial Profiling.
Look at the picture to the right. Are the character all different races, if so what are they? Are they all the same race, if so which is it?
It can cause some other problems with a Live-Action Adaptation... do you cast a character based on canon ethnicity or just someone who falls in the range of their 'stateless' vagueness? (See the controversy around the live action movies of Avatar The Last Airbender, Dragon Ball and the upcoming AKIRA for example).
People typically fall back on one of two explanations for this trope.
The first is that the purpose of mukokuseki is to make characters look distinct so that the audience, and the artists don't get confused. In works set in the largely homogeneous Japan, it can be hard for an animator to make unique designs in a such a simple art style for several dozen straight black haired, brown eyed people.
A bigTrope Codifier for this was Sailor Moon. Going down our main cast list, we have two blue-eyed golden blondes, a blue-haired trope codifier in her own right (with blue eyes, natch), a dark-red-head, and a reddish-brunette with green eyes. All of them, to a girl, are 100% unblemished Yamato in ancestry - (In the Live Action version they addressed this by making the hair and eye colors part of their transformations. Out of costume they were all normal black or brown haired Japanese girls.) SM's influence on Japanese pop culture helped to spread the look a lot and it now pervades all mediums (anime, manga, advertising, videogames etc)
The second is the idea that the artists are appropriating features from the exotic 'other' (in this case Causcasians) into their character designs either for their own interests or for marketing purposes. To that point, the pervasiveness in Japanese pop-culture of physical features such as fair hair, blue or green eyes, pinkish skin and chiseled facial features which are not found amongst the homogenous population of Japan arguably suggests such features are considered fashionable, desirable and interesting. This is overall more common with shoujo or josei series, because a lot of the earliest and most classic shoujo, such Candy Candy and Rose of Versailles, took place in Europe or America.
On the other end of the spectrum from the Sailor Moon example, the creator of Naruto, Masashi Kishimoto, went on record saying he was happy Naruto was designedwith blond spikey hair because after the series went international it made the character more relatable to western audiences. He later stated that for a live action version, they'd need to cast a white American actor to play Naruto (despite him being ethnically Japanese) to ensure a good likeness, so he's sticking with his story.
Regardless of what they look like, assume that the character's race matches the original primary audience unless its heavily implied (through setting, culture, costume or Word Of God) to be otherwise. That's true of all media that doesn't use Facial Profiling Eastern or Western, even Literature when you have to use your own imagination. But it can really be either explanation, or both. Without Word Of God it can be hard tell, which is why some people unfamiliar with the concept come to the conclusion that Japanese people have rather a skewed sense of self-perception.
Arguably started by Osamu Tezuka, whose art style was heavily influenced by the works of Walt Disney, Max and Dave Fleischer and other American cartoonists. However Big Anime Eyes do have a somewhat Asian slant to them and aren't as round as Big Disney Eyes and Big Looney Tune Eyes. That's part of the reason you don't confuse Red Hot Riding Hood or the Disney Princesses for anime characters, even Rapunzel.
Compare Ambiguously Brown (when someone in Mukokuseki has noticeably different look from the rest of the main cast, but still has no distinctgiveaways or mentioning of any race) and Only Six Faces (where there is little difference at all in character designs).
It would probably be easier to list Japanese comics, videogames and anime that don't indulge in pure Mukokuseki, so....
Exceptions to this trope:
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Anime and Manga
The human characters in InuYasha (which takes place entirely in Japan) are all realistically Asian (black hair, brown eyes), although, admittedly, this is more prevelant in the manga than the anime.
The same can actually be said about any of Takahashi's series. Ranma ½, Urusei Yatsura, even RIN-NE (save for the red-headed Rinne Rokudo himself), all feature better-than-average depictions of Asians.
In Azumanga Daioh, the characters from different areas of Japan look believably similar to the real-life skin-tones/hair colors. However, there is orange-haired Chiyo-chan (although redheads are known to exist naturally in Japan, they are exceptionally rare, and not without some gaijin mixing or genetic anomaly.)
Averted with AKIRA, where everyone (save the foreign troops) looks convincingly and realistically Japanese.
The original Mobile Suit Gundam's Mirai Yashima & Hayato Kobayashi are fairly Asian-looking compared to the rest of the cast. Series protagonist Amuro Ray, who isn't may get a pass, as he's part foreigner, his mother being either American, Canadian or Mexican depending on the version.
0083's Kou Uraki is often commented on as being the most Asian-looking character in all of Gundam.
Most of the characters in Nadia: The Secret of Blue Water are European whites and look the part, with pinker skin and such. All of the characters of different races look like their respective races. The only exceptions are the Atlantean characters, who are a sort of brown skinned mukokuseki, somewhere between Indian and African.
Originally Nadia (and Atlanteans by extension) were going to look realistically sub-Saharan African, but the animators could not get Nadia's original hair to move to their satisfaction, so they threw the design out and started over.
Most of Naoki Urasawa's manga are drawn very realistically. The Caucasian looking people in his work actually are Caucasian (with huge noses though), as many of his manga are set in Europe or other exotic locales. In fact, Urasawa occasionally goes too far in the other direction. Monster 's Eva Heinemann, a German, has a slightly Asian look to her. Just about the only time he plays this trope straight is with Kana from 20th/21st Century Boys, who has more of a typical big eyed, fair haired "anime girl" look to her, resembling Monster's Anna/Nina, but this is probably to emphasize the character's "otherness", as she has supernatural powers.
Also played somewhat straight with his redesigns of many classic Osamu Tezuka characters for Pluto, especially Ochanomizu & Tenma, due to their comedically oversized schozzes, which could never be reduced to typical Japanese proportions without rendering the characters unrecognizable. So while they do look realistic in a sense, they don't look like people who could realistically be named Tenma or Ochanomizu. Shansaku "Mister Mustachio" Ban also suffers from this, as his character model was recycled from Monster's Dr. Reichwein, who is in turn based on the American actor Wilford "Diabeetus" Brimley. Urasawa does a surprisingly good job on Inspectors Tawashi & Nakamura, though, as Well as Astro Boy & his "sister" Uran.
That being said, Dr. Tenma, of Monster fame, who is supposed to be Japanese, is drawn stylistically very similar to several characters who are supposed to be German, even if his skin and hair color are realistic.
Usually played straight with Ojamajo Doremi, but there are a few exceptions. In the episode where Momoko receives a video letter from her Black Best Friend Beth in New York, Beth's new friend Sachiko is drawn with narrower eyes to highlight the racial differences between the two girls.
Fullmetal Alchemist mostly avoids this, as it takes place in a Fantasy Counterpart Culture of central Europe and visitors from the east like Ling are stereotypical Asian-looking for the most part. The few black characters like Paninya also have noticeably Nubian features. It also inverts this trope with Roy Mustang, who looks more like somebody from Xing than Amestris. Fanon has it that his mother is from Xing, but within the manga this is never commented on.
Since his foster mother has been shown to be madam of a brothel there's no knowing which of his parents could be from where. Also worth noting is Izumi also sports a much more Asian in appearance then the rest of the cast as well, and not to mention has a distinctly Asian first name amongst a cast that has predominantly Western names even despite her Western maiden name, "Harnet". Like Mustang her ethnicity has yet to be commented on. Note that since Amestris does sport a variety in race in its population it might not be considered worth commenting on by the rest of the cast.
Compare Mustang to many, many other characters in the series, and it becomes noticeable that while he loves to mention Ed's shortness, he himself is actually not very tall. He's only a little taller than most of the women, and shorter than all but two of his subordinates. Combine this with his Asian-esque eyes and pitch black hair, and it becomes very likely that he does have Xingese ancestry.
A curious inversion occurs in Patlabor. While it plays this trope straight to varying degrees with the main cast, in order to emphasize Kanuka Clancy's otherness she was drawn as the the most Japanese-looking.
Oddly played in Cardcaptor Sakura; Syaoran and Meiling are somewhat more obviously "asian" than most of the rest of the cast (likely because they're Chinese, rather than Japanese) and Sakura's brother Toya is also rendered in a far more "asian"-looking manner... which often makes it look like he and Sakura aren't even related, because Sakura herself follows the trope straight almost all the way to the hilt.
A few other characters manage to avoid the trope as well, Clow Reed as an example. As does Syaoran's Hot Mom, Li Yelan. (Her five children excepting perhaps Syaoran himself, however, all play the trope straight; obviously, they take after their late father.)
Windy Tales uses a Korean art style where the characters are very clearly not white.
Chang Wufei in Gundam Wing looks recognizably Chinese. Heero Yuy falls squarely into this trope, being Japanese but possessing generic features and blue eyes. A more obvious example is Quatre who is supposed to be Arabic, but is a blond haired blue eyed bishonen.
For years Fan Wank attempted to explain Quatre by saying he's Berber; more likely it has to do with his mother being Caucasian, blond, and blue-eyed (with Fan Wank again stepping in to claim she's French). Heero, on the other hand, is revealed to be half-Russian in the novel Frozen Teardrop.
Setsuna F. Seiei from Gundam 00 is an odd case, looking vaguely Japanese before it's revealed that he's actually Kurdish and that's simply a code name (real name: Soran Ibrahim).
On the other hand, Saji Crossroad who, despite the surname, is supposed to be Japanese looks not too dissimilar to the American Graham Aker, or Irish Lockon. Setsuna, on the other hand, is clearly a very different nationality than they are, and his skin tone is far more suited to Middle Eastern skin tones than he is to Japanese.
An odd example in Michi Ko To Hatchin. The major character Atsuko is half-black and half-Japanese, and yet has blue eyes and (apparently) naturally blond hair.
Averted with most of the other characters. There are tons of black and Latino characters with dark skin and features, and most of the non-mixed Asian characters have recognizably Asian facial features as well.
The characters in series illustrated by artist Takeshi Obata really do look Japanese.
Light Yagami, the main character in Death Note, has a thoroughly Caucasian appearance when compared to the other characters. His mother, father, and sister are all obviously Asian. He is depicted with common European traits, like white skin and light brown hair. Misa is also depicted with blue eyes and dyed blond hair, though she's never described as a white person. In the original manga, her eyes are brown and her hair is dyed.
Between that series and Sasami: Magical Girls Club, you get a lot of non-Asian-looking Asians due to the cast keeping their Tenchi Muyo! looks despite being normal Japanese people instead of long-lived Human Aliens. Mind you, it's that or everyone becoming unrecognizable.
Pretty much everyone in Genshiken is recognizably Asian, and the only two light-haired characters explicitly dye their hair. The two American characters who visit in the second season are also distinctly Caucasian.
Sue looks more like an American-styled cartoon character than an actual American.
In Ghost in the Shell most characters look more or less as if they could be actually Japanese, depending on the art style of the different artists/animators. Except for Batou and Togusa, who don't look asian at all. Most of these can be justified in that most of the cast are heavily modified cyborgs, with Batou and the Major (at least) basically being robots with human brains. They could look like any race at all, and in Motoko's case, even her original sex is up in the air.
The Twelve Kingdoms starts off in Japan, and people look decently Japanese. Youko's reddish hair is called out from the beginning as natural, unusual, and inexplicable. There's a mysterious blonde, then another one, but they have reasons, as is revealed after the action moves to the fantasy world, where people explicitly have anime-diverse hair and skin colors. Dark skin, red eyes, purple or orange hair, it's all there (and in the original novels). (But not many blondes.) Youko herself transforms to scarlet hair, emerald eyes (vs. a gray or very dark green in Japan) and brown skin.
Most of Tsutomu Nihei's manga have several distinctly Asian-looking characters, although considering the trans-human leanings of most of them, this could often be more an issue of personal taste than ethnicity. Nihei even pokes a bit of fun at racial differences in Blame!! when Japanese-looking hero Killy passes through a land of blonde people who are all at least twice as tall as he is.
Somewhat averted in Soul Eater, where the predominance of caucasians is justified by Shibusen's being located in America. Concurrent with this, there are several black characters as well.
In Digimon Tamers, Henry Wong looks distinctively Chinese with his yellowish skin tone, thicker eyebrows and sharp eyes.
In Digimon Frontier, there's Izumi Orimoto, blonde with blue eyes. Her backstory is that since she lived in Italy for most of her life so perhaps this was a deliberate coloring choice to accentuate her "differences" from other Japanese kids. For the record, the other Chosen are relatively dark haired/dark eyed with different skin colors.
Digimon Xros Wars features Kiriha Aonuma and Yuu Amano, who both are this without any explanation. Even more confusing, Yuu's sister Nene is decidedly not an example herself, having brown hair and a slightly darker skin tone.
There are a substantial number of Japanese characters in Area 88, two of whom are at the eponymous airbase. Can you tell who they are without knowing names?
Black Lagoon does relatively well. The assassin Shenhua (a.k.a. "Chinglish") actually looks Chinese. Mr. Chang is an Expy of Chow Yun-Fat as a shout out to John Woo films. Hotel Moscow do not blend visually into the Southeast Asia setting. The Japanese characters arguably look relatively more Japanese than everyone else, but still fall under this trope. And Chinese-American Revy began with very narrow eyes but quickly took on this trope within the first chapter, and there's a theory that one or both of her parents may not have been entirely Asian.
Cowboy Bebop has a wide variety of ethnicities and there is considerable effort to make them appear properly ethnic. Some of the terraformed planets have an architectural Planet of Hats with corresponding cultures like Morocco, Ecuador and Vienna. In fact, some fans theorize that Spike Spiegel is Jewish.
Neither does the gun that he uses being from Israel
Despite being largely responsible for this style, Osamu Tezuka himself has a few aversions. A few of his recurring characters, most notably Tonan Shipan are more distinctly Asian than most. Tezuka also often used an interesting workaround. When depicting his ostensibly Japanese characters traveling to the Western world, he would often exaggerate his foreigners' appearance; Tezuka's Westerners are usually taller than his Japanese characters, with wide shoulders and long noses. This is especially noticeable in Black Jack.
This is mostly averted in Adolf, wherein the German characters and the Japanese characters look noticeably different.
Well, when Ginko was designed the writer was imagining the story set in the modern era, with the first story set in a traditional house deep in the woods, but it somehow slipped into an alternate feudal era, leaving him with his anachronisms. At least according to the author's notes. But then, he's supposed to be a freak, anyway.
The hair and eye(s) are justified: they're the result of a mushi.
The cast of Great Teacher Onizuka tends to look authentically Japanese but most of the young female characters are subject to Generic Cuteness, though to a lesser degree than usual. The manga has been advertised as "NO big eyes, NO magic powers, NO giant robots".
Similar to something mentioned above, there was a segment in the manga the depicted Chinese people in a more realistic (stereotypically Asian) manner than the characters, as part of a racist joke involving the hiding of illegal laborers, no less.
Darker Than Black is a mixed bag. The Japanese characters are all over the place. Kirihara looks Japanese whereas all her co-workers have the Mukoku Seki look. Most of the episodic side characters, such as Chiaki (ep1-2) or Mai (ep3-4) also look ethnically ambiguous. The main character, Hei, is an interesting example of both averting and playing this trope straight. When using his civilian disguise as Li the Chinese exchange student, he has Mukoku Seki features such as wide eyes. However, when he becomes Hei, his eyes narrow and become sharper, and his appearance becomes more plausibly be Chinese. April and Babo both have recognizable African features, though.
Most of the characters in Sayonara, Zetsubou-Sensei have a somewhat normal Japanese appearance, with the obvious exceptions of Kaede Kimura and Taro Maria Sekiutsu.
Also to considered are the OVA movies; Kenshin comes off way more Japanese in those, but there is also a large shift in art style to consider.
Tokko - Though they all have Japanese names, this is especially obvious when Ranmaru and Muramasa are seen together.
Welcome to the NHK - All the characters are recognizably Japanese. The only character with blond hair is obviously bleaching it, since we see flashbacks of her in high school with dark hair.
Code Geass seemed to be trying to avert this trope in theory, especially since race and racism were major plot points, but its Britannian lead was designed so he could have been Asian (or a space alien), and its most major Asian character so that he could have been Causasian, and one of its most flagrant racists' right-hand man had a British name (Guilford) but an extremely Asian appearance.
Then there is Kallen Kozuki/Stadtfeld, the daughter of a Britannian nobleman and a Japanese woman. On the one hand she attends an elite Britannian academy. On the other she's a major member of the Japanese insurgency well before the Black Knights get going. It seems like one side or the other should have questioned her mixed heritage.
Of course, both seem to know. For the Japanese insurgents, their nominal leader - until Lelouch gets involved - is an old friend of Kallen's brother, and has known Kallen and her fully Japanese mother for well over a decade. Lelouch, of course, just doesn't care. By the time people who would be more strict about that get involved, there's the much more blatant C.C. and Diethart. On the other hand, when Milly finds out, she catches on to the idea that Kallen is trying to hide it - more Kallen's father and step-mother, really, but that's pretty much how it seems to be. However, Kallen's most striking features are her red hair and blue eyes, which are quite Caucasian, whereas her Japanese features are... indeterminable.
The Chinese who don't just look weird look Chinese, though, and most of the minor Britannian and Japanese characters look Anglo/Aryan or Japanese. Or like aliens.
You're Under Arrest!'s cast is pretty clearly Japaneses. Though they still have eye-colors which aren't really possible with Japanese people.
Downplayed in Neon Genesis Evangelion. Ritsuko has blond hair, but flashbacks showing her in high school make it clear she dyes it. Asuka has reddish (or brown depending on the adaptation) hair and blue eyes, but this is explained by her having a white German father, and she's mentioned as looking "exotic" by several other characters. Rei and Kaworu both have red eyes and pale skin (with Rei also having blue hair) but this is implied to be the result of being created from Angel genetic material.
Rebuild of Evangelion 2.0 starts out in a European/Russian NERV base under attack; most of the personnel in the base clearly are Caucasian (except for Kaji).
Mari Illustrious Makinami has blue eyes and brown hair, but Word Of God states this is because she is half-English.
If the movie takes place in Japan, Hayao Miyazaki's characters tend to have dark hair and eyes. Fair-haired people crop up on occasion in the backgrounds, but most of them only appear if the setting is meant to be European.
Averted in BECK. To keep with the indie-film feel, the whole cast have rather realistic hair colors and rather look Asian. Of course, the series throws in a couple Black people and a few Whites for contrast.
Kyo Kara Maoh is set alternately in modern Japan and a Northern European sort of fantasy world, where the Japanese main character gets a lot of attention for having black hair and black eyes. As does his older brother, eventually, who's less cutely designed and therefore more clearly Japanese. However, he still falls under the "big eyes" design. The Germanic looks of most of the main characters are noted in the first episode, while the lead is still finding his feet and has no idea what's going on, but afterward they don't really come up, since they're standard to the world they're in. Also some fantasy coloring like pink are green hair, and a couple of vaguely Asian-looking people here and there.
Like the third season's inexplicable soukoku Berias. Spoiler tag hides major twist. Who turns out to have been concealing his actual identity as a blond elf prince.
Played straight with the main character's mother (who may be Japanese-American although she's now living in Japan), who has curly light brown hair and generic cute features, though in one flashback scene in Boston she refers to herself as Japanese.
However, if asked about their ethnicity, most Americans would not answer with "American". They'd respond with the less obvious answer, naturally.
In Flag, the cast is multi-national and this is reflected in the design of the cast. The Japanese and Chinese characters look different from each other and they do not look anything like the American, European, African, and other Asian cast members. The inhabitants of the fictional country look like a cross between Indians and Nepalese.
Hanazakari no Kimitachi E, or Hana Kimi, is set in a Japanese private school where the ethnicity of the characters is obvious, especially whenever the manga-ka bothers to color in their hair. Main character Mizuki is half-American and given light brown hair, and her friends commented upon seeing her blond-haired blue-eyed brother that he looks more American- to which she replied they were actually half-siblings.
Osakan classmate Nakatsu is obnoxiously blond but is given a backstory wherein he explains why he dyes it.
The Dorm 3 RA Himejima seems to be a stereotype of French overdramatism and flamboyance, even carrying around a rose, having long blond hair and appearing with shoujo sparkles- but he is explained to be a half-German who worships his European heritage.
Mizuki's friend Julia has very blond, curly hair and blue eyes, which garnered lots of attention when she arrived in Japan to visit her.
In fact, the author seems to relish getting the chance to draw more than Japanese people, so there's a high number of blondes, blacks, and more when the characters visit California.
Banana Fish does a good job making the different character's nationalities apparent in the art.
Project Blue Earth SOS has a very multi-ethnic cast and each cast looks appropriate. Earth SOS's character design even averts the large eye phenomenon, the eye size is normal.
All the characters in Gokusen including Kumiko actually Japanese. Even the many Gonks have that asian look to them.
Chrono Crusade is a bit of an unusual aversion—there are characters with strange hair and features that don't seem to fit under any particular nationality, but they're not human at all. The characters that have blond hair and blue eyes are all Americans, but there's also Americans seen with brown and black hair. Two German characters have red and brown hair, respectively. There is a White-Haired Pretty Girl, but she has red eyes and is probably supposed to be an albino (and she is supposed to be a little strange, as well). On top of this, in the manga a minor character appears obviously Japanese next to the Caucasian characters.
Most of Junji Ito's characters look quite realistic, though he has a strange habit of giving his main female characters slightly more European-looking hair & eyes (most notably Kirie from Uzumaki). The funny thing is, though, that because of his art style, these features look slightly unusual with the rest of their faces, giving his women a somewhat unreal, doll-like sort of beauty. Come to think of it, most of his heroines look an awful lot like Kristin Kreuk...
In Sword Of The Stranger, the Chinese and European warriors all look significantly different from the Japanese. However, the title character somehow manages to hide his non-Japanese ancestry merely by dying his hair.
Noir does well with this. Especially noticeable since the main characters travel around the world doing their job, you see the differences clearly.
A few characters in Eureka Seven are distinctly Asian-looking. Talho Yuki is a bit of an odd case. Her Japanese-sounding surname gives the impression she's playing this trope straight to a degree, then we meet the slant-eyed, small-boned Rei and wonder what the heck Talho is supposed to be, since she's certainly not what Rei is...
∀ Gundam has a truly weird inversion. One of the Moonrace officers looks like he was drawn by a completely different artist than the rest of them, closer to the way Japanese people are drawn in American comic books: small eyes; short, rounded nose; dark hair (in a samurai-esque topknot, even!). His name? Phil Ackerman. There's also Po Ai Zhi (or something like that), who looks more or less like somebody who would actually be named that. Most of the cast is either Caucasian-looking or Ambiguously Brown, though. The funny thing is, there doesn't seem to be anybody with a Japanese-sounding name in the cast. Big Bad Gym Gingnham likes to dress up like a Samurai, but he's just a huge weeaboo.
Combined with Phenotype Stereotype, in Samurai Champloo a one-off character was eventually shown to be from Holland and merely visiting Japan. The characters only notice he was a foreigner because he had light/wavy red hair and blue eyes. Otherwise the difference between him and all of the other Japanese characters was almost unnoticeable.
Real Drive: The eyes are small, hair is brown, and everyone's body looks realistic. That is, they don't look like rail-think crack addicts.
The odd thing is that, while the girls' facial structures are more Asian-looking than typical anime girls, their figures are suspiciously foreign-looking. Most chubby Asian girls tend to carry more weight in their busts and bellies, while the RD babes are more bottom-heavy.
Dragon Ball's Taopaipai has a Chinese-ish name and he does indeed look Asian. However, other characters with Chinese-inspired names (Like Goku or Tenshinhan) don't. Justified with Goku and Tienshinhan, though, because they're actually aliens.
Dr Slump has to convince his backwater grandpa that his blonde, blue eyed wife is in fact Japanese. He isn't entirely convinced claiming that the eyes and hair ain't proper.
Hachimaki in Planetes looks distinctly, almost stereotypically Japanese, with the yellowish skin, wiry black hair, and slanted eyes. In contrast, Tanabe is also Japanese, but her complexion is indistinguishable from the Caucasian characters; however she is adopted and her birth parents' ancestry is unknown.
Done somewhat in Eyeshield 21. All the Japanese characters have black/dark brown hair and brown eyes, the ones who don't have clearly colored their hair since their eyebrows are still black. Interestingly, none of them are ever draw with an eyelid fold either (though they still have rather anime style eyes).
However, when it comes to facial features, it's a no holds bar of weirdness. For example, a Japanese player who loves Egyptian culture actually LOOKS like an Egyptian, rather then just a really tan Japanese guy. The only prominent character whose drawn with Asian features is Seijirou Shin and that's because he's based off Bruce Lee.
While played straight in Shaman King, some of the non-Asian characters, especially Silva, have narrower eyes than the Chinese and Japanese characters.
In Ai Yori Aoshi, the natively Japanese characters have a "yellower" cast to their skin than the American Tina (except for Chika, who's darkly tanned). This is particularly noticeable when Aoi and Tina are seen together. Of course, all characters regardless of race have anime-style eyes and (save Kaoru, Chika, and Tina) unnatural hair colors
Parasyte characters look very Japanese, especially Mori Uda.
Durarara!! characters are convincing as the two other foreign characters (Celty and Simon) are designed differently. Any character with blonde hair is shown to have dyed it.
Rushuna of Grenadier appears and is even assumed to be foreign because of her blonde hair and huge bust.
The Wandering Son characters are all noticeably Japanese. Everyone has either Black hair or Brown Hair, and everyone has either Brown Eyes or black eyes. The anime adaptation subverts this though, as they gave essentially everyone new eye colors (typically Technicolor Eyes).
In Mai Hime, while most characters are straight examples, Natsuki, in the side novel, "Natsuki's Prelude," finds it suspicious that "Yamada," her informant, "didn't look Japanese at all," and suspects that Yamada is not his real name. Yamada briefly thinks back to the time in the service of "his country," but it's never revealed where he is from.
In YuYu Hakusho, every human looks realistically Japanese, with standard black or brown-variation hair, except for Kuwabara and Kurama. Kurama's odd red hair color is likely a result of altering the genes of the human fetus he possessed. In Kuwabara's case, his hair looks like the result of a Japanese person dying their hair blonde without bleaching it first. This was actually a common trend among Japanese juvenile delinquents in the 90s. This trope is completely averted in the manga, however. In colored manga images, Kuwabara and Kurama both have standard black hair.
Averted with a VENGEANCE later in Slam Dunk which carries on into all of Takehiko Inoue's works. Most of the characters look unmistakably Japanese, and the ones that don't are quickly acknowledged as strange looking. The main character himself has epicanthic (single) eyelid folds and a somewhat wide nose, making him look the most Japanese despite having bright red dyed hair. On top of that, most of the characters in the show are far from fair-skinned.
As in You're Under Arrest! (by the same author), there's a distinct effort to make the characters in Ah! My Goddess distinct racially. Belldandy and her sisters (goddesses suggested to be of stock similar to Europeans) have larger eyes than all of the Japanese characters (though some females come close), and Bell and Skuld have paler skin than any of the Japanese characters as well (Urd doesn't, but that's addressed when it's revealed that she's half-demon).
Full Metal Panic characters, while a very diverse group, range from realistically drawn to not resembling anyone.
Who the hell knows with Hunter × Hunter; while obviously not in the real world, the given map is an upsidedown anagram of a real world map, and some locations have (polictically) relative equivilants, based on looks and names, but there's no way to determine anyones supposed ethnicity. Names espcially seem haphazard in distribution.
In the manga, all Japanese and Chinese characters are depicted with what one would assume is either black or brown hair, and are generally differentiated by their style of dress (although Ranma prefers to wear Chinese-style clothing normally).
In the anime, this is done a bit more subtly - the Japanese characters do have either black or brown hair (or dark blue in Akane's case). Most non-Japanese characters will have some other hair color (blonde, purple, green, pink). Exceptions include Azusa Shiratori, whose hair is more of a darker honey color, and the black-haired, Chinese Mousse.
G Gundam, operating as it does on Captain Ethnic, predictably averts this for most of the Japanese characters. The exception is blue-eyed brunette Rain Mikamura (though it's within the realm of possibility that her mother, who is never mentioned, is of a different nationality.)
Naruto for the most part plays this trope straight, but averts it with the Uchiha clan. All the Uchiha have black/brown hair, black eyes when not activating the Sharingan, and narrower eye shapes, making them the most Japanese-looking among the Loads and Loads of Characters.
There are actually quite a few secondary characters who look relatively East Asian, such as Shikamaru, Choji, Shino, etc. The Hidden Cloud Village also has a lot of African-looking characters.
Partially averted in Princess Jellyfish. Kuranosuke has blue eyes and blond hair, but this is due to him having a blonde, Caucasian mother. It's remarked in-story that he looks absolutely nothing like his half-brother Shū, who is a full-blooded Japanese man with typical Asian facial features and coloring.
Strike Witches averts this trope to some degree. Japanese characters are shown with realistic black to lighter brown hair color and yellowish skin color. Other races gets corresponding hair and skin color such as Finnish character has light skin color and British character with reddish complexion. Played straight with the facial features, none of the characters have ethnic facial features.
Axis Powers Hetalia gives appropriate hair and eye color to the European and Asian characters, though it does have some artistic breaks via Technicolor Eyes and heavily indulges in "Westerners areblond". Some Westerners have uniquely foreign features, such as Russia (large nose, large...everything else), France (wavy hair, lots of body hair), Spain (curly hair, olive skin, "clear cut features typical of Spanish"), Germany, Prussia and Sweden (squinty eyes, a common trait of anime westerners). For the Asians, Japan's straight black hair, short stature, Older Than They Look appearance and dark, almost soulless eyes make him stand out from the Europeans, and China has slight Tsurime Eyes. Played mostly straight with the skin colors, everybody who isn't a shade of tan or brown has the same pale pink skintone. The first four seasons of the anime take this to an extreme, leaving only Cuba with darker skin while "neutralizing" the olive-skinned Spain, Romano, Greece, Turkey, the Arabian Egypt and mostinfamously, the Creole-African Seychelles. The anime's fifth season fixes most of this (except for Greece, who is rendered bizarrely pale and blue-eyed when he was close to Turkey's coloring in the manga). It even adds more variation; American has a slight tan, England is more pale, China and Japan are given yellowish/ocher skin, etc.
In Ouran High School Host Club, the blond-haired and blue-eyed Tamaki appears to be just a conventional instance of Mukokuseki. It's later revealed that he's the illegitimate child of a Japanese man and a white French woman.
Detective Conan versus Lupin III has an egregious example. People from Vespania are portrayed with varying hair colors (while Japanese people in the series all have dark hair), and all the trappings of Vespania are European in style (although no location is explicitly mentioned). Yet Ran, who is Japanese, is a double for the princess of Vespania.
The in-game character models in Final Fantasy X follow this trope. However, the FMV ones have very noticeable Japanese features—for some of them, at least: Rikku is quite obviously Asian, as is Tidus, and Yuna is noticeably Asian but with slightly softer features. Wakka is Ambiguously Brown. Lulu, Auron, and Seymour, though, are white as the driven snow. These may have somewhat to do with their lifestyle rather than their race, though.
In some scenes from the early concept trailers for Advent Children, Cloud looks rather obviously Asian. This was changed to the more racially ambiguous look (i.e. European in hair and eye color but with epicanthic folds and a mix of facial features) he and most other characters have in the final version(s) of the movie, as well as Dirge of Cerberus. This also arguably the case for both the early versions of Sephiroth and Kadaj.
Overall, most Final Fantasy characters, have Western eye and hair colors, but Asian facial features.
An odd variation on this occurs in Megaman Battle Network with Dekao "Dex" Oyama, whose comparatively dark complexion & full lips give him an oddly negroid look, rather than the 'stateless' features typically given to anime characters.
This only gets weirder with his little brother Chisao, who, in sharp contrast, has very light skin, beady eyes, and a body shape that resembles nothing so much as a Bobble-Head. We don't know what the Oyamas are supposed to be, honestly.
Zettai Zetsumei Toshi very noticeably did not use this for virtually the entire cast... making Agetec's attempt to Westernize it (they never quite realized it's not 1994 anymore and you don't need to do that) by giving a huge part of the cast blonde hair when they released it as Disaster Report painfully transparent. The sequel uses it a bit more, making the Westernization a bit less blatant.
The Persona series has characters that have consistent Japanese traits in contrast with the few Western characters (that is if you could look past the odd hair colors). Apparently, the characters in the first game looked so Japanese that the localization had to Photoshop them in order to make them look more "American".
Certain characters in Pokemon and its adaptations to an extent; Kanto being the most realistic, with almost everyone having realistic hair colors and eye colors for a Japanese person, and anyone who doesn't either fits into Ambiguously-Something or is American. However, starting in Johto this trope was played straight more often, with plenty of blond and other light-haired characters who are clearly Japanese. In Unova, it's hard to tell who's Asian and who's not. You'd expect the ones with Japanese names to be so, but one of the more well known cases is back in Kanto, which is realistically drawn and colored we have a red haired, blue eyed girl with a Japanese name.
Harvest Moon takes place in a European, or American, setting. This trope is usually subverted. A majority of characters are white, and when characters of other races appear it's apparent. However, a few characters are Ambiguously Brown.
With the addition of Tale of Two Towns, we finally have a town full of vaguely Asian-looking characters. The other eponymous town, however, is a typical HM town.
The early Sakura Wars games (set in Japan with a largely Japanese cast) play this straight, but Sakura Wars V (set in New York with a largely non-Japanese cast) averts it, with the two major Japanese characters, Shinjiro and Subaru, being noticeably Asian-looking in coloring and features.
Siren models all the game's characters after Japanese actors, complete with their real life faces, making this game as absolute an aversion of this trope as one could find.
Street Fighter typically averts this trope well, but certain characters still slip into it. R. Mika and Karin from Street Fighter Alpha look European, especially the former, however are apparently Japanese.
New character Natsu, debuting in the Soul Series's fifth main iteration, was born in 16th century Izumo, Japan and sports entirely incongruent strawberry-blonde hair and unambiguously western facial features. Her incongruity is compounded because the other Japanese characters, samurai Mitsurugi and Natsu's predecessor Taki, sport racially correct black hair and brown eyes.
It's a stretch but she could be related to Setsuka, who by the way is a natural blonde non-Japanese living in Japan.
Given how the Soul Series usually averts this, it's possible — nay, probable — that Natsu is just a foreigner who was raised in Japan, just like Setsuka. She doesn't even have to necessarily be related to Setsuka, either (much like how Arthur wasn't). Why people keep thinking that she's playing this trope straight and not a foreigner is a bit baffling, actually, not to mention the fact that nobody brings up Yun-Seong's bright red hair or Maxi's blondness in his alternate outfits. Though even they have Asian features, whereas Natsu is notably very Western-looking in facial structure.
It's a double-edged sword for Natsu: If she is Japanese ethnically, then that is ludicrous as she in no way shape or form looks it and is the very essence of this trope (this seems likely as the developers specifically stated Setsuka was Western, which they have not for Natsu). If she is Western (and it just hasn't been stated), then that's equally grating as it makes her the series' THIRD blonde, Western pseudo-Japanese castaway living in Japan at the time - surely the designers don't need to resort to Mukokuseki / But Not Too Foreign principles THRICE when creating "Japanese" characters?
This is of course debatable as the concept art in progress was trying to give the Darcsen a Romani look. The designers apparently got fed up with the accusations that they had to introduce a Japanese-expy character into the third entry to show that the Darcsens were not a stand-in for the Japanese. Whether or not you think they're telling the truth is also a matter of debate.
Canon Foreigner You Ji from Bladestorm The Hundred Years War completely (and pleasantly) averts the Mukokuseki principle - his look is unambiguously and realistically East Asian, amongst a cast of caucasian English and French characters. It's arguably a double aversion in You Ji's case, as Bladestorm originates from the Koei stable, who are notorious for employing Mukokuseki principles across their hero-series Dynasty Warriors, where auburn/red/light-brown/blond haired, green & blue-eyed asians abound in ancient China....
It wasn't until Dynasty Warriors 7 that they played the Mukokuseki card straight. Before that, only one character was actually blonde (apparently trying to replicate the ganguro look).
It's not just the blonde hair (and incidently, Xiaoqiao with honey blonde hair and Zhurong with platinum blonde were around in 5), it's also the unambiguously western facial features. Sure, some characters do look realistically asian, but there are an equal amount who, like Yueying◊, have the chiseled facial features of caucasians.
Homestuck would be a rare Western media example. The "playable" human characters are rendered with completely white skin, while actual Caucasians (like Andrew Hussie's Author Avatar and Dinosaur Comics authour Ryan North) are rendered with not-quite-flesh-tone skin that's more orange than anything. Word Of God has specified that the blank white characters are supposed to be a-racial, so it's left up to the reader to decide what race they are.
Spoofed with Dave being a "white rapper". Briefly got changed to gibberish when fans wanked about it, but changed back later.
In You Got HaruhiRolled!, Kyon has a Freak Out when he realizes that he is the only character in the series who looks remotely Japanese. After he runs out of the room, Itsuki asks Yuki, an alien, if she is supposed to be German or something.
While he doesn't mention this trope by name or even in the context of manga per se, Scott McCloud does give his insight into what he thinks is the operating principle behind this trope in his comic book about comic books Understanding Comics: When a person's image is presented in an iconic, abstract fashion, it encourages the reader to identify with that character and see part of themselves in him or her.
This blog post entitled "Why do Japanese characters look white?" considers two possible reasons for Mukokuseki. The first is that anime characters don't look white to Japanese people (because the assumption in Japan is "Japanese unless marked otherwise" instead of "Westerner unless marked otherwise" like Westerners are used to). The second is the heavy importation of Western culture to Japan after World War 2.
An old YouTube video, entitled "Are anime characters Japanese or Caucasian", argued that large eyes and pale skin are not necessarily Caucasian traits. Though the video has since been removed, some of the responses remain.
Mukokuseki is cited by M Night Shyamalan to justify the Race Lift of characters in The Last Airbender. Unfortunately, Avatar is one of the cartoons it least applies to. While there are some ambiguous features and rare eye colors, most Avatar characters have a generally Asian look, or Inuit in the case of the Water Tribe. Most tellingly, there are no blonds and a grand total of two redheads in their world.