Thief and Black Mage in 8-Bit Theater, who regularly have to deal with the stupidity and crazy "logic" of their companions Fighter and Red Mage. Especially Red Mage, self-professed genius. Considering that characters like Fighter, Red Mage, Black Belt and even Thief have shown the ability to do things that violate the laws of physics simply by ignoring them, one of Black Mage's reactions is a pleading, "How? Seriously, how?" Quite often, Black Mage flies into an impotent rage and stabs the perpetrator in the head if the sheer crazy gets to him; or his mind seeks solace in temporary clinical insanity. Black Mage still hasn't gotten over the pitiful and futile habit of trying to argue sense with the universe. Black Mage has on occasion acknowledged that Thief is the only one beside him who is sane, and vice versa:
Black Mage: So, Red Mage, enlighten us. How can a plan that makes no sense work? Red Mage: One simple reason: It makes too little sense to fail. BM: What. RM: Most plans are critically flawed by their own logic. A failure at any step will ruin everything after it. That's just basic cause and effect. It's easy for a good plan to fall apart. Therefore, a plan that has no attachment to logic cannot be stopped. The success or failure of any given step will have no impact on the macro level. BM: That's so stupid I can't even see straight anymore.
The fact that not only are his team-mates insane or Too Dumb to Live but even the world occasionally usually makes little or no sense certainly doesn't make him feel any better.
This is the schtick of Atomik Lad in particular in Nuklear Age. While Mighty Mettalic Magno Man and Rachel are also sane, the former is often a witting accomplice to Nuke's insanity, while the latter is generally more interested in watching. Atomik Lad notes in the Court Segment that perhaps he is the insane one, because everything would make more sense that way.
Ardam in Adventurers! questions — and often strongly objects to — the inexplicable physics and plot-related idiosyncrasies that exist in his world. Although these objections are perfectly intelligent and reasonable in the real-world sense, they're of no practical use to his situation, making him ultimately an example of Wrong Genre Savvy. Karn, the main character and his best friend, is the reverse — he's Genre Savvy, but tends to come off as a bit of an Idiot Hero (often BECAUSE of being Genre Savvy).
Ardam and Karn seem to switch places early on, in that Karn started the sane one and learned the logic of the land, whereas Ardam accepted the madness but went sane later on.
Cherry from RPG World is another example of a character who doesn't quite grasp the video game logic she is living in.
Reluctant sidekick Paul in Man-Man is the only one who really sees that an non-powered idiot in a costume doesn't make a superhero, that renting the basement to your cheese-fixated evil-genius nemesis is a strange idea, that ideas have downsides or that in his world "superhero/villain" appears to be a synonym for "nutcase".
Roy, from The Order of the Stick, typically takes this position at various points throughout the comic with his level-headed views. The Sanity Ball often trades hands in OotS, generally to whoever's more experienced, grounded, or alive at the moment.
Durkon for a time seems to be the sane one of the part of the group with Hinjo, though he passes it to Hinjo himself every so often and takes his time worrying about the tree army sneaking up on him.
Celia is even more so, due to basically being a normal person who doesn't really like to fight or kill. No wonder she hooked up with Roy. Celia seems like the sane person in the party, and moral too... right up until she starts strictly applying naive, kindhearted moral choices to situations with thieves' guilds and mad scientists mages. Once she starts trying to use "Can't we all just get along?" style speeches to murderous cutthroats, her position of sanity degrades rapidly.
Haley is the sane one in her mini-group. But almost everyone gets their turn at pointing out how crazy everyone else, or the world, is being, so it might be that any adventuring group is only allowed one sane person at a time. As she said while caught between Stupid Good Celia and Stupid Evil Belkar, "I wonder if the gods would be offended if I just prayed directly to Roy for strength not to strangle them both".
Redcloak is most definitely the Only Sane Man in Team Evil, being the only non-Mook who is not evil for evil's sake, a childish epic-level monster, a goth with a crush on her evil skeletalsorcererboss, or a wisecracking insect with no regard for the [lack of a] Fourth Wall. Granted, if you've read Start of Darkness you know Redcloak has issues too, but the others have subscriptions.
Redcloak's brother Right-Eye was so sane that he eventually abandoned Team Evil entirely to attempt peaceful co-existence with humans. He was doing pretty well too, until Xykon showed up again.
In The Inexplicable Adventures of Bob!, Bob would fit this trope if not for the fact that he is, totally unintentionally, the cause of most of the insanity around himself; and that he is now getting pretty used to it. His girlfriend Jean epitomizes this trope though, and is always capable of taking a few steps back and recognizing the absurdity of Bob's problems — an acuity which invariably makes her life more difficult, as she must still deal with those problems even while recognizing how nuts they are.
Zoë used to take on this role during the early years of Sluggy Freelance. She's still usually the most grounded member of the cast, but over time she's gotten used to the bizarre characters and events that fill her life.
Jayden and Crusader's character Crusader started out as strange as the rest of the cast, but slowly has flipped to playing the straight man in a household which involves a particularly violent atheist with no sense of humour at all, a mentally insane former-assassin and a possibly insane, possibly time-travelling scientist who wears a top hat, acts like he's from the 19th century and has been known to breed man-eating anteaters.
Recently Crusader has been acting a little insane again because, in the words of the creator 'Crusader hasn't been crazy for a while. I decided to rectify that.'
Oh, it's Florence. She's constantly having to fix problems caused by Sam and Helix, and most of the other characters exhibit very odd personality traits (kleptomania, unchecked bureaucratism, enslaved to programming...) which she has to deal with.
Chloé in Frivolesque is arguably the only "normal" girl among the five main characters. Much to her chagrin.
Dimo in Girl Genius plays this role to his slightly loopier fellow Jagers, Oggie and Maxim. Consider the following exchange (with heavy Funetik Aksent), on Gil:
Maxim: Hy vill teach him how to impress de gorls! Oggie: Hy vill teach him about de birds und de veasles! Dimo: Und hy vill teach him how to avoid those two.
Violetta: You mean to tell me that you knew that guy by name on Castle Wulfenbach, and it never occurred to you that this guy, with the same name, might be the mystery son the Baron had been hiding all these years?!
Klaus Wulfenbach is essentially the Only Sane Man to the whole of Europa.
Moloch Von Zinzer repeatedly plays this role with all the Sparks surrounding Agatha Heterodyne.
In this strip, a nameless soldier is the only one not immediately convinced that Gil is who he says he is just because Gil has an impressive hat.
Gil: (punching said soldier out) "Once all this is settled, you get a promotion."
Krosp plays this constantly. Odd that the only sane man is a cat.
Central to the premise of Ursula Vernon's Digger, which makes great play of this as a racial characteristic of wombats in a universe where folklore is living history and 'magicked-up' tunnels are occupational hazards. More specifically, it follows the adventures of one young wombat dumped via hazardous tunnel into a world featuring a god in chains, talking statues, living shadows, oracular slugs and homicidal vegetables. Among other things.
Aeris in VG Cats seems to be the sanest. Mind you, this is by comparison to:
In Casey and Andy,the only sane one usually alternates between Mary and Jenn.
It's Mary, seeing as how Jenn thinks nothing of being inter-dimensionally kidnapped for two weeks and then carrying on a conversation that, from the other person's point of view, has only been going on for less than a minute.
The Space Pirate newcomer to Planet Zebeth is serving this role, seemingly being the only Space Pirate-affiliated character in the entire comic who actually remembers that they have any kind of mission or organization (as opposed to Ridley, who's opened a bar, Kraid, who just gets drunk and chases Samus around (not necessarily in that order), and Mother Brain, who hasn't really been doing much of anything lately).
Kaitlyn Hu from Precocious. Her time spent observing the others has built up remarkable insight into the social dynamics of the class. She employs this to great effect starting in this strip. The ensuing conversation provides her with justified time in the spotlight.
In Platinum Grit Kate Provocski is the only major character able to comprehend that all the impossible things going on around them are... well, impossible. And she's really starting to stress about it.
Sloan of Snowflakes gets put in this position a lot, though she's not without her own neuroses.
Kanaya's counterpart Porrim fills this role for the Beforan trolls. The rest of the group consists of an agent of dark forces (Kurloz), a guy with severe brain damage (Mituna), a Large Ham trying to hide something about herself she doesn't like (Latula), a generally nice guy who just happens to be a pushover (Rufioh), two Jerkasses (Cronus and Damara), two obsessives (Aranea and Meulin), an obsessive jerkass (Kankri) and...Horuss, who is just kind of weird and crazy.
For the Alpha-universe humans, it turns out, surprisingly enough, to be Roxy. Dirk is a massive pile of issues and clinginess, Jake is clueless, self-centered, and a bit of a jackass, and Jane is suffering from both the Batterwitch's brainwashing and severe teenage angst. Roxy, who's mostly not involved in the convoluted love triangle, is left to look on in bemusement and try to sort out everything herself.
Best demonstrated during the Trickster Mode debacle, where Roxy's reaction to having two of her friends turn up, apparently high and possessing superpowers, is "oh dear god" followed by hiding.
Parson Gotti, aka Lord Hamster, in Erfworld. Somewhat justified since he was summoned in a world where physics follow the rules of a turn-based wargame. Lampshaded by Jack Snipe in book 2 :
Lord Hamster: Yet the enemy hasn't attacked her yet. And that's because...?
Jack Snipe: Because... it wouldn't be Noble.
Lord Hamster: Right, because the enemy is crazy too. Got it.
Jack Snipe: Indeed. As a sane man, you are badly outnumbered again, my good Lord. Perhapes you should defect, and join us all.
Jack Snipe: Bravo, lord, 'twas a splendidly speedy defection.
He generally seems to be the only person on Erfworld who really understands strategy at all. No-one else seems able to cope if their initial plan fails or plan much more than stacking bonuses, with the possible exception of Charlie.
Although Jack has seemed to take to the idea like a boat to water.
Jack: "Lateral Thinking." For that wonderful phrase alone he was forever in his Lord Hamster's debt.
Space Hojo and Son Gohrotto in Twisted Kaiju Theatre often play this role. They appear to be the only two members of the Toxic Pirates who aren't lunatics, idiots, or assholes.
Snippy in Romantically Apocalyptic. Although Engineer fits this trope to some extent too, Snippy is the one who mostly has to deal with the Captain and Pilot's insanity, and is for the most part sarcastically accepting of his role.
Sonichu has Magi-Chan, who is the only one that doesn't kiss Chris's ass all the time. Though there are some unfortunate side jobs of his All There in the Manual.
D'artagnan in Ghettonauts seems to be the only character capable of non-surreal thought and intelligence. He suffers for this.
In Ménage à 3, sanity tends to be contingent at best:
Junghan and Amber have both played this part briefly, but never really settled into it. Minor character Allie sometimes looks like an only sane woman when she's talking to her colleague Sonya.
Gary might qualify if he wasn't so often the Butt Monkey and/or the Accidental Pornomancer. However, he has his own issues that might exclude him from the role anyway.
New character Peggy demonstrates how this trope is performed here. A little later, in the May 09, 2013 strip (#739, NSFW), she perhaps realises that she's got the job. Her first scenes (which involve her dumping a bowl of pasta over her boyfriend's head in the course of breaking up with him) suggest a degree of flakiness of her own, but by the standards of the comic, she's a beacon of sanity.