Not a main character, but Kimblee in Fullmetal Alchemist wears a white suit all the time, and gets upset with a soldier for being blown up while talking to him, not to mention the small amount of blood spatter that ends up on his pristine suit. Kimblee's barking mad. He says that it is expensive at one point in Brotherhood.
The illustrator Takeshi Obata thinks of L as Neat Freak, which is why he chose to depict him as such (the writer, Tsugumi Ohba, didn't tell him to do so) and made him grab things with the tips of his fingers. Does not extend to his personal experience (he might well sleep in his clothes. In his defense, they look comfy).
According to Gevanni's observations, Teru Mikami is also this (which fits his overall personality pretty well).
Chiri from Sayonara, Zetsubou-Sensei has this as her gimmick. And she's been slowly Flanderized from a simple Neat Freak to a near psychopathicControl Freak who'll be perfectly willing to slaughter the cast in order to maintain order. Any scene featuring her as centerfold for the scene will inevitably result in comedy and scary moment. In one of the OVAs we're introduced to her older sister, Kitsu Tane, who is her complete opposite and great character foil. We have it explained that in their childhood, Tane chose to become The Pig Pen and personification of the Trash of the Titans trope in order to save the life of their gold fish, which Chiri had decided to clean... With shampoo...
Hazuki Oikawa from Moyashimon. What a disinfectant-happy girl like her is doing at an agricultural college (and hanging out with people who study microorganisms for a living, at that), we're not sure.
As an extension of his Super OCD, Death the Kid always makes sure everything is neat, tidy and, most importantly, symmetrical.
In the Legend of Zelda: Four Swords Plus manga, Blue Link is revealed to be one of these in an omake. It's impossible for him to sleep at night unless his clothes are neatly folded and in a nice neat stack near where he's sleeping.
Ranma ½: Not overly shown to be a Neat Freak, but Ranma finds himself compulsively tidying Hinako-sensei's apartment (twice), forgetting that he sneaked in to steal her fighting fish in manga volume 30, chapter 5.
Eiichirou from Baby Steps eats from both sides of his lunch box to keep the sides even, freaks out over the possibility of his food touching, and takes two sets of notes in class: a pristine "master" copy, and a second that he doesn't mind lending out to his less tidy classmates.
One chapter of Franken Fran has a woman, raised in extremely sterile circumstances, recruit Fran in an attempt to wipe out cockroaches. She freaks out at the merest hint of contamination. The experiment does not go as planned...
In "Black & White", Ash and Co. run into a Minccino who is obsessed with cleaning dirty things. It steals Ash's badge case to clean it and most of the episode is revolved around trying to get it back. This proves difficult due to Minccino's elusiveness and speed. Just when it's about to runoff, Bianca, Professor Juniper's lab assistant, pulls out a dirty Pokeball to catch it. Knowing couldn't pass up the opportunity, it decides to clean her Pokeball and ends up getting itself caught.
Ash's Mom owns a Mr. Mime who's a neat-freak too, keeping it in the house as a sort of maid. It's been known to run its vacuum over Ash's face as he sleeps if he doesn't wash it.
In the Sailor Moon manga Sailor Jupiter is shown to be this, at one point spending two days cleaning her apartment.
As is obvious once you get a glimpse of his meticulously clean, almost-empty apartment, Barnaby from Tiger & Bunny does not appreciate clutter. He keeps only the bare minimum furniture; one chair, one small table, one bed etc., and the only "unessential" objects in the living room (the one room we see properly) are a laptop, a television (both of which he uses to research his parents' murder), a family photo and a toy robot (a birthday present from his parents). He also dislikes the thought of anyone visiting his place, worrying that they'll make a mess.
Nami Yamigumo of Silent Mobius is the AMP's resident neat freak. Unfortunately for her, most of her teammates are the exact opposite. This is played up in comic omake strips.
Charles and Ray Beams in Eureka Seven keep their ship impeccably clean at all times. One of the first signs of Ray's breakdown after Charles is killed is the fact that the ship has been utterly trashed. Things just get worse from there.
Inverted in Fruits Basket: Machi can't stand when things are spotlessly clean. She frequently messes up clean rooms and such because she can't stand the "perfection".
In "The Neat Job," from the first issue of EC Comics's Shock SuspenStories, a man drives his wife over the edge with his obsessive demand that everything in the house be stored in a precise location and manner, even requiring her to keep a running inventory. In the end, when he berates her for breaking a jar of nails, she goes Ax-Crazy on him and then places each of his body parts in carefully-labelled jars.
Jacques the French cleaner shrimp. It's all in the name.
Gurgles appears to be more of a germophobe than an actual Neat Freak, but when they're deliberately making their tank dirty, he's the most distressed by it. Jacques, aside from some small difficulty fighting his cleaning urges, isn't overly stressed.
Patricia C. Wrede's Enchanted Forest Chronicles has Morwen, a witch who lives cleanly enough to subvert the "Kill Witches With Water" stereotype.
Mr. Standish from The Long Dark Tea-Time of the Soul is an eccentric variant: a clutter-averse man who keeps his phone, intercom, and personal ornaments sealed up inside his desk, leaving every horizontal surface in his office absolutely bare. The picture frame on the wall is empty, and he has to open a desk drawer every time he wants to check his notes.
Jace in the Mortal Instruments series. Clary notes that his room is as neat as a pin. When he is rooming with Magnus Bane, the poor messy warlock is driven nuts by Jace fixing up his apartent.
Tris in the Circle of Magic series. The various relatives she was fobbed off on during her childhood made her earn her keep by housekeeping, and when she first comes to Discipline she corrects the other kids' attempts at it. She makes a point to pitch in with the chores in whatever house she's visiting.
Seemingly everyone in Star Trek: The Next Generation. Whenever anyone notices anything out of place, they point it out instantly, and it always turns out to be a major plot point. Likewise, no messes are ever seen aboard the Starship Enterprise. They're on a starship; a large one but still a starship. It's a closed environment. Anything that spills and gets left out eventually gets into everything and there are some really high-tech gadgets all over the place that could be affected by being gummed up. It is confirmed in "Up the Long Ladder" that the ship is self-cleaning; the mechanism for this is never described.
Sheldon on The Big Bang Theory. There's an episode in the first season where, seeing the messy state of across-the-hall-neighbor Penny's apartment, he sneaks over in the middle of the night while she's sleeping to clean.
Leonard: Sheldon, this is not your home.
Sheldon: No, this is not anyone's "home"! This is a swirling vortex of entropy!
James May on Top Gear, who keeps a paintbrush in his car to clean the air vents and gets uneasy when things are out of order. Most likely has some degree of obsessive-compulsive disorder. Mocked by Clarkson via application of a watch bezel. If it's not aligned to the right point he'll forcibly try to sort it out. The result was jokingly compared to Kryptonite.
Danny Tanner from Full House fits this trope, so much so the trope could be named after him. He thinks of big spring cleaning as an equivalent of Christmas.
Monica Geller in Friends, who (amidst many, many other things) can't sleep after she willingly leaves her shoes in the living room in order to prove she's not as much a Neat Freak as everybody thinks. Everybody's right, of course. Or she vacuumed her vacuum cleaber with a smaller one, and that one she vacuumed with another even smaller.
On Saturday Night Live, one of Phil Hartman's reoccurring characters was the cooking-show host "The Anal-Retentive Chef", who painstakingly cleaned up every last scrap following each step in the recipe of the day.
Cat in Lip Service to the point where she is considered autistic.
In Buffy the Vampire Slayer, The Mayor often delivers little speeches on the importance of cleanliness (including clean fingernails), keeps thing neatly aligned on his desk, and abhors germs.
In the background, when they're filming in the main M5 shop area, you'll often see one of the signs Jamie made, reading "Clean Up Or Die".
Claireparker from Pixelface. In "Reset", she explains that because everything in her game is so dirty and broken, she feels compelled to keep the console as neat and perfect as possible.
Subverted with Sylar on Heroes. Flashbacks show that he kept an eerily clean and organized apartment with plastic covered furniture. But when the second he snapped and began murdering people, he had no qualms about getting dirty to get what he wants. He also had emptied out and cleaned his apartment with amazing speed after realizing Mohinder had discovered evidence of his crimes.
Ricky Fitness of The Aquabats! Super Show! doesn't like getting dirty and keeps sanitation products with him at all times; his Handi-Gel defeats Dr. Eva Mudlark's muck monsters in "Laundry Day!" but his Wet Naps don't work against a monster who is made of lint and cleaning chemicals.
Abner of Hanna Is Not a Boy's Name is highly mysophobic and OCD, to the point of wearing a surgical mask and gloves as a preventive measure.
JoeyVonKrause from Mortifer. It's probably OCD, as he really hates being touched as well. This also figures into the plot: a throwaway line from "William" ("How they expect me to work in this filth is beyond me") about his perfectly clean office is a clue as to his real identity...
Connie of Waterworks is downright germophobic, to the point where being splashed with what she thinks is toilet water sends her into a murderous rage.
Alfred in Batman: The Animated Series. When he and Bruce briefly visit some run-down movie-store, Alfred tries his finger on the counter, reproachfully looks at the dirt it comes up with and then proceeds to wipe the counter clean (well, cleaner) with a cloth.
Alfred from Batman the Animated Series later appears in Justice League'', having still retained this problem. After an attack squad of Thanagarians barge in to attack the League in the Batman, he's seen dutifully sweeping up the enormous mess they've made as the team head out to make their assault. "Mind the broken glass, sir."
F.O.W.L. agent Ammonia Pine from Darkwing Duck. (Ironically, she had a sister named Ample Grime who was the opposite, a complete slob. Even more ironic, the two siblings made quite an effective team in one episode - until the end where both villains were apprehended, at which point they started flinging insults at each other.)
Dexter's mom in Dexters Laboratory. The episode "Pslyghtly Psycho" suggests that she is actually germophobic, particularly when her gloves and slippers are removed and she finds herself afraid to even set foot on the carpet barefoot.
Zim of Invader Zim at one point become this after realizes (incorrectly, by the way) that Earth was covered in germs that could quite possibly kill him. He then goes on a cleaning spree, even going as far as tying Gir onto a tree outside because he was so infested. At the end of the episode, he's seen wearing a "suit" of meat since the meat itself was designed to be sanitized for space travel and, thus, germ-free.
Rarity displays this at times, especially in the episode "Look Before You Sleep". She hates getting dirty, folds bedsheets a precise way, and spends her time picking up and positioning fallen trinkets instead of focusing on the huge tree that has crashed through the window. Her attention to detail helps solve the problem, though.
Played with in "Sisterhooves Social" when Rarity discovers her sister Sweetie Belle has organized her "inspiration room", which was previously messy and gets completely outraged. Sweetie Belle comments about how Rarity now "likes" messes, to which Rarity clarifies that it was "organized chaos" on her end, which plays into her being an artist/fashion designer. At first still pissed about the supposed lack of inspiration, a short time later Rarity comes up with an idea for a full spectrum clothing line based on how Sweetie Belle organized the different colored fabrics.
Rocko from Rocko's Modern Life is a subversion in that while he does like his house clean, he often does let cleaning fall by the wayside. While he does produce Trash of the Titans, he always cleans it up...with hilarious results.
Chuckie from Rugrats is shown to be this way, which is Tommy's breaking point after spending a week with him in one episode. Chuckie ends up taking it to a major extreme in another episode, where he dons a germ-proof "suit" and attempts to force the babies not to play anything to keep clean. Tommy and the twins quickly get him out of that phase.
An episode of My Dad The Rock Star has Willie meeting his new girlfriend's parents. They throw away the flowers Willie wanted to give them because they came from dirt, they spray the tracks he leaves and have everything wrapped in plastic (including the dog).
Porky Pig in The Looney Tunes Show. His reorganization of Bugs's house in "Gossamer is Awesomer" drives Bugs round the bend.