About half the cast of Bleach trade off doing this. EspeciallyIchigo.
Keaton Yamada, the narrator of Chibi Maruko-chan. He often has harsh words for the schemes, thoughts, and actions of Maruko and her grandfather. He gets increasingly Flanderized in this role as the series progresses.
C.C. from Code Geass. Her caustic remarks are about the only thing which can rein in Lelouch's overinflated ego.
Lelouch himself dishes out the snark as well towards C. C.'s more insouciant tendencies, among other things.
Spike Spiegel from Cowboy Bebop is an unusual example in that he is a Deadpan Snarker given the role of the main character of an action show and is a defining badass in anime. He retains his hero status despite his snark because Faye fits the role of Lancer in most episodes.
Yamcha: This coming from the guy who was beat senseless by Cell?
Tien too. When Android 18 came to Kami's Lookout Yamcha tries to scare her off (While keeping his distance).
Yamcha: Gohan's here, and he's stronger then Cell so why don't you get out of here.
Tien: Um... why don't you come a little closer and say that?
Speaking of Android 18, her sarcasm is one of her most defining traits. When asked if her real name is legitimately "No. 18", she responds "My father was pretty dull". (In the original version, she replies "That it doesn't matter" before tossing the number at the World Tournament Announcer). She was kidding, by the way, her birth name has never been revealed. (Until recently. It's Lazuli.)
Goku is this at times to prove he isn't as stupid as people think he is.
Demon King Piccolo: I'll only need to defeat you in five seconds.
(Demon King Piccolo attempts a chop at Goku, only for him to catch it and throw him into the next building. Piccolo then angrily emerges from the rubble.)
Goku: By the way, it's been five seconds.
Misaki Matsuya from Excel Saga manga is a powerful example. Once she renders Iwata and Watanabe into howling fits of laughter with a single deadpan sentence. It's made pretty clear that under her stoic exterior lies the heart of a master humorist. Unfortunately her anime counterpart didn't get a chance to test her skills in this field. Excel herself also shows signs of this trope.
Fate/stay night's Archer, who has nothing but utter disdain for idealism, particularly in regards to his counterpart Shirou.
Rin and Shirou definitely snark a lot too, though Shirou keeps his comments to himself most of the time. Remove his politeness to keep his mouth shut and you get Archer.
The Hinooka sisters from Fire Girl. The younger one more so than the older one. Orie Kujou and Takumi Touya count too.
Riza Hawkeye in Fullmetal Alchemist. A high-ranking aide to Roy Mustang, she acts as both his conscience and the voice of reason on his staff, despite sometimes seeming to exist only to keep the other characters (including Mustang) in line and point out their shortcomings. She does snark in the manga, but always politely.
Ed gets his share of snarkiness as well, often towards Mustang (and vice versa).
Taka: [breathes heavily into the phone, having unexpected Saikawa to pick up, rather than Ryuuichi] Kamitani: Talk, you idiot! State who you are! What are you, a pervert? . . . [takes the phone] Ah, I'm sorry. It's me. Saikawa: If you're asking about my underwear, it's black today.
Kiyomaro Takamine tends to fill this role often in Zatch Bell! due to his genius and the outright oddity of other characters' plans (usually Folgore's) that somehow work.
Lots of characters from Gintama, especially Yorozuya trio, since good deal of the comedy is based on deadpan comments. But the snarkiest of them all has to be Okita Sougo. Almost everything that comes out of this guy's mouth is deadpan iced with lots of snark.
In JoJo's Bizarre Adventure, Jotaro's sense of humor tends to manifest in very blunt, matter-of-fact ways. For example: casually writing up a bill for the inevitable beatdown Steely Dan will suffer (as well as a receipt once it's done).
Jotaro: It's your tab. I have to make sure you pay me back, but I'm forgetful, so I'm writing it down.
Tomoe from Kamisama Kiss seems almost incapable of opening his mouth without letting at least one sarcastic comment out.
Marginal Prince gives us Henri, who has the art of snarking perfected to the point where the other characters will even lampshade instances where Henri isn't present to snark at his favourite target, Alfed.
Henri: That's all right. Your stupidity is infectious. Alfred: You're saying my stupidity is infectious?? Henri: Well, you were born like that.
Ruri Hoshino of Martian Successor Nadesico does this so often that she, just like the examples in Western Animation and Live-Action TV, used to have a trope named after her.
Gaara becomes one in the Five Kages Conference responding to the Tsuchikage:
Tsuchikage: The makeup of the Five Kages sure has changed. It's hard to believe someone as young as yourself can become a Kazekage. Your father must have trained you very well, but you seem to be lacking in manners, boy.
Gaara: You're right. And yet here I am, as the Kazekage.
There are three types of characters in One Piece: Deadpan Snarkers, madmen, and Total Idiots. Sometimes characters will wear different hats (e.g. Usopp, who occasionally plays the fool, or plays snarker to Luffy's idiocy). Many characters share multiple roles, switching back and forth between them, and there are very few characters who are completely serious such that they display neither any ounce of stupidity or some snarker tendencies at some point.
Haruhi Fujioka from Ouran High School Host Club is a magnificently brutal snarker, especially where Tamaki is concerned. It helps that she often doesn't seem to realize that the things she says tend to hurt people's feelings. It also helps that she's apparently unaware of how fond the rest of the host club are of her.
The anime turns the main character (named Yu Narukami) into this one, looking deadpan even if he's being kicked to a waterfall. Most of the humor involving Yu comes from the fact that it's hard to tell when he's kidding or being serious. For example, giving this line about one arguably homosexual underclassman after "accepting" him.
Kanji: Sempai, didn't you accept me!? Yu: Not at night.
The Persona 3 movie turns the protagonist, Makoto Yuki, into an even bigger one.
Makoto: You chained your nose to your face so you won't lose it.
Jessie & James: (wearing ridiculous dance outfits) This has to be our greatest plan yet! Meowth: Dat's what worries me.
In Best Wishes Ash's rival Trip is a very snarky individual. However, most of his comments goes toward Ash only.
Trip: That voice can be heard on the opposite side of the street... (after Ash demands that he battle him, completely ignoring the comment made)
Trip: Humans usually don't try to capture themselves in a Pokéball. (after Ash gets in the way of him trying to catch a Palpitoad causing Trip to accidentally hit Ash in the face with said Pokéball)
Ash himself actually has a lot of Snarky lines throughout the original series.
Misty: (about Snorlax) It looks like it's going to be sick! Brock: Well how would you feel if you got kissed by Meowth? Ash: I'd get a new mouth...
Misty had some great snark too.
Gary: (to Ash) Ash, I've never seen anyone so pathetic! Misty: Have you looked in a mirror?
Bonnie in the XY series has plenty of these moments, mostly regarding Clemont's inventions.
In Popcorn Avatar, this is the only way Kurando can get back at Lisa, as he's unable to really do anything else.
Although in the first season of Princess Tutu Fakir was much more of a Jerk Ass, in the second season he calmed down a bit and started to swing into this trope.
Ahiru: Good morning, Fakir! You're up early! Fakir: Early for you, anyway.
The manga version of Ranma from Ranma ˝ is a Deadpan Snarker; his anime incarnation is not really one. Nabiki from the same series has her moments, though it is a much larger trait for her in Fanon than Canon and in the anime than the manga.
Saito from Rurouni Kenshin has plenty of these moments. Kenshin himself often fits this trope; more so in the manga than the anime, as the anime is often dangerously close to overusing his oblivious act.
Aoshi, in the manga, takes the "deadpan" part so far that the snark can get lost in translation.
Artemis, mainly by virtue of living with the borderline insane Minako. His best hit comes in Codename: Sailor V, where Minako always claims that her newest crush is her first love... And at one point he not only whipped out a sign congratulating her for her 1,000th first love, but in the last chapter he feigned springing a surprise party on her to celebrate her 5,000th first love.
Luna, also an alien cat with a crazy protege, has her moments too, but she's more likely to shout at her.
The (almost) eternally-deadpan Kobushi Abiru of Sayonara, Zetsubou-Sensei. She usually wears a neutral, bored expression on her face (or as much of it as can be seen under the bandages), occasionally uttering a cutting line to another of the students in her class while they're talking about something. In chapter 19 of the manga (volume 2 in tankobon), when Kotonon the heavily-photoshopped net idol is outraged over being called a fat-ass and nobody-has-ever-been-so-mean-as-to-call-me-that, Abiru quips "What? Not even once?" with a perfectly straight face (and tone of voice in the anime, IIRC). Many of her lines can be interpreted as being snarky; occasionally Nozomu-sensei receives some of this snark too, though more recent episodes have depicted Abiru to be more often smitten with him.
Sekai Ichi Hatsukoi gives us Ritsu Onodera because he's jaded about love, doesn't much care for his job as a Shoujo Manga editor and not happy that his boss, Takano, just so happens to be his ex first love. Takano is also very snarky as the no-nonsense head editor. There's also Kisa Shouta who's also jaded about romance and life in general and Yuu Yanase who's experiencing unrequited love.
Gourry in the original Slayers novels. With a healthy dose of Obfuscating Stupidity as well. Applies more to Zelgadis in the anime. Gourry is deadpan, but that's usually because he's serious and there's no hint of snark.
Dai-Gurren begins filling up with water Leeron: So much for the quick fix...
Hiroyuki Fujita, the main character, from To Heart seems to fit in this category, although it seems to be a result of his laziness and the fact that he wants to "eat, play arcade games, and sleep the rest his life away". Despite his dry attitude, laziness, and tendency to tease girls who annoy him at times, he shows his sympathy through his actions rather than his words, no matter who it is.
Nagase: In any case, if she does come out, we'll have to do something. Lemmy: Okay! The Astral Busters are on the job, right? Hiroyuki: Why do you have to attack her? When she appears we're going to talk to her. Lemmy: Is that so? Hiroyuki: Were you even listening to us before?
Domeki in ×××HOLiC, who seems to have the unusual ability to always maintain a deadpan and monotone expression no matter what happens in order to add to his snarking ability. Unless, that is, Watanuki is actually being serious and introspective, at which point he can't think of anything to say. Such as when Watanuki stupidly trades his eye away to help him or announces that he is taking of the shop until Yuuko (presumed dead, but there's reincarnation and stuff) returns.
Kaiba: Anyone who is late to my tournament will be disqualified. Mokuba, make sure Wheeler's late.
Gozaburo: I treated you better than my own son! Kaiba: Thanks for nothing.
Yu-Gi-Oh! GX: Kaiser Ryo is quite snarky. It's more obvious in the dub, but he gets in a few in the original.
[a massive beam of light explodes from the sky] Aster: Something's happening. Zane: You think? What gave it away, genius?
In Yu Gi Oh Zexal, Astral alternates between being incredibly naive (like the Innocent Alien he resembles) and needlessly sarcastic, sometimes both at once. In fact, it's often hard to tell whether his sarcasm is intentional or not. For example, in the dub version, he says this after Cathy's duel with Dog-Chan:
Astral: Observation #18: People say dogs are a man's best friend. Yuma would make a good dog.
Note that his observation has a somewhat different meaning in the original version.
Yako in Yurara, especially towards Mei. Mei snarks right back at him, but is less deadpan about it.
Kurama and Hiei in YuYu Hakusho, with Hiei being an out-and-out jerk and Kurama being a bit more subtle. They're at their best when they're snarking at each other. Yusuke does this sometimes as well, as part of his wisecracking routine.
In the manga-only ending, when Kurama is mistaken for a female several times, then asked to help with a case at an all girls' school, and he asks if he need to do something as a disguise (Yusuke was already snuck in once) or just go as is, Keiko remarking to Yusuke about how scary Kurama was. Each time you can't see his face, making the mood even weirder.
Kanon (2006 anime) has Yuuichi Aizawa. Many comparisons are made between Kyon and Yuuichi, especially because of a few similarities in appearance and having the same seiyuu. However, both characters are vastly different; whereas Kyon makes such comments to himself, or intends only himself to hear, since he is usually bored or silently shocked at the "stupidity" around him, Yuuichi openly states such comments to tease his friends. Yuuichi's snarky commentary usually translates into good-natured fun and flirting rather than disdainful commentary.
Yukito from AIR also demonstrates snarkiness but it may just be that since he is quite mature, his attitude of common sense and practicality contrasts even more when he is surrounded by childish females.
Tomoya Okazaki of CLANNAD likes playing pranks on anyone gullible enough to fall for them (Sunohara in particular - it's implied he does it just to see if he'll fall for them). He does this with a completely straight face, which makes it all the funnier. However, he seems to make such comments aloud only to mock others. He's not above making wry comments either:
Sunohara: When the time comes, Okazaki, I trust you to watch my back. Okazaki:(Enthusiastically) Lucky! I'll be sure to stab you well.
Dazai Osamu is a master of this trope in Bungou Stray Dogs in Chapter 31 of the manga.
Chuuya: *looks at Dazai with an annoyed expression in his face* Don't walk next to me.
Dazai: *with an annoyed look on his face* Aren't you the one walking next to me?