In Angels 2200, Quetz ends up asking this to herself. When Hammer sneaks into her hospital room to check on her, Quetz rather than being appreciative or even concerned for Hammer, contemplates pressing the call button on her bed to summon help in an attempt to get Hammer caught and removed as commander of Icebreaker Squad, unaware that they already know she's in here because of surveillance cameras. Hammer talks Quetz down by telling her that if she betrays her, no one in Icebreaker will want to follow her. Quetz then questions herself as to why she didn't press the button, and ultimately concludes that it's because she wants to belong.
Arthur, King of Time and Space: Morgan of Gore, aka Morgan la Fey, Arthur's half-sister the would-be usurper asks herself one in the science fiction arc.
The Beast Legion , when Master Surya asks Xeus, whether he'd last for two blinks against Dragos.
Darths & Droids: While Obi-Wan and Yoda are discovering the Jedi Temple massacre:
Ben: Sally, this is serious. You need to play it seriously. Sally: Just because you do everything Dad tells you to! Ben: What? No I don't! Sally:Why are you studying medicine then?!
In Dubious Company Sal accidentally does this by saying: "Of course I have a home. Doesn't everybody?" By the looks on Walter, Tiren, and Elly's faces, those words were devastating.
In Evon, in response to Hero protesting that his feelings for Evon are strictly professional, his friend Felvis asks him if that's the case, why is he still with Evon, protecting her, since the job she originally hired him for (retrieving her father's spellbook) was long since done.
It may be subjective, as it's an all-caps comic, but there seemed to be an undertone of intense worry there; "Yes! Of course the glass plates we're eating off of are clean. We use only the finest window cleaner on them... Oh, Crap!."
In Girl Genius, as Tarvek prepares to escape Sturmhalten with Lucrezia-Agatha, inadvertently asks one of these of her. "It's difficult, leaving... all this behind, not knowing when I'll return. You ever get like that?" He doesn't see her reaction, but the expression on her face is one of the few times we see a real emotion on Lucrezia's face.
TT: Have you ever looked into the sky without your shades?
When Terezi starts sharing her concerns and doubts with Dave, he is unsure how to respond. He finally asks "Do you want me to tell you to be a better human or a better troll?" She avoids actually answering the question.
Parodied when Rose and Dave finally meet the trolls in person. With most of them acting like idiots, an embarrassed Terezi claims they're usually cooler than this. Dave asks "are you really?" and after a moment she admits no, they really aren't.
Lil Hal springs one of these on Dirk when the latter is attempting to kill him.
TT: I am scared to not exist. TT: Aren't you?
Gaia: King Savos has one for Gaia's chosen, San de Vertis:
King Savos: "Has it crossed your mind that you may also be one of Eldor’s magic machines instead of Gaia’s chosen one?"
During the "No Cure for the Paladin Blues" arc, Elan asks Roy why he likes Miko. What makes this noteworthy is that since her introduction, most of the team have been vocal about her displeasure of her, but Roy manages to shrug off or ignore their complaints. Then comes Elan who flat-out asks Roy why he like-likes her and Roy can only come up with her being attractive and of the same alignnment before Elan uses simple logic to come up to a potential conclusion and then a question that Roy cannot answer... He's actually happy they're attacked before he could answer.
Elan: I was thinking. Why would Roy LIKE like a girl who is so mean to his friends, and I can't figure it out. Unless you like her more than us. Is that it, Roy? Do you like Miko more than you like me?
Slightly Damned: Without quite realizing it, Sammy asks Kieri to think about Buwaro's feelings for her, and their recent falling out. The question... stings.
Spina Cage: "Hasn't anyone ever depended on you?" seems to be one for Joven.
At the start of Three Apples, Applejack tries to cheer up her little sister by explaining that Cutie Marks mean more than simply their appearance. Apple Bloom then asks what AJ's mark stands for, throwing her sister for a bit of a loop.
Apple Bloom: So what's three apples? Applejack: Pardon. Apple Bloom: Your three apples. What does that make you— ripe?
In the second act, Apple Bloom hits her with a harder one by asking, "Does anybody like you, Applejack? \ Are you anyone's favorite?"
In Serenity Rose, this is done three times in as many pages when we're shown excerpts from the documentary "American Gothic"; The creator of a trashy, unoriginal comic is asked how many goth comics he's actually read after he continually derides them, the bassist of a goth/punk band is asked whether every fashion statement has to be political after she repeatedly rails against teenage girls who only subscribe to the lifestyle superficially, and nihilistic maniac superstar Rivet Hed is simply told straight up that "In the 16th century, they burned people like you at the stake."
Nebula: After a long argument trying to get Saturn to agree to hand over their moons, Uranus finally demands to know what would happen if they just reached out and took the moons, if Saturn would actually try and stop them. After a long, tense moment, Saturn admits that no, they probably wouldn't.
In the lore of Kill Six Billion Demons, the Hot-Blooded goddess Aesma poses one of these to YISUN, the Top God who created the universe, and it's remembered as the only time in existence that YISUN hesitated. When YISUN tells her in typical gnomic fashion that the universe is not a self-evident truth, she pitches a fit and asks "Then what is it?"
"My opinion", said YISUN, finally.
Megatokyo: Just as Miho's about to crash headlong over the Despair Event Horizon following the horde attacking her at school and seemingly killing Piro in the process, Kimiko stops her short with a question that causes Miho to question her entire perspective regarding the futility of fighting against her "story", which has killed and resurrected her countless times over the years.
Kimiko: What about what happens to you in his story?
In Season 3 of Survivor: Fan Characters, a livid Montana is about to dump the tribe's supplies into the fire after the other contestants unexpectedly voted out her best friend N over her, until Violet asks her if N would want her to throw away her chances of winning just to get revenge which causes her to reconsider.
Sans: Did you ever enjoy it? W.D. Gaster: Excuse me? Sans: Did you ever enjoy hurting us? W.D. Gaster: ...I do what I have to do. Sans: That's not an answer... But it's the only one you got, isn't it?
In the MLP fan comic Trixie Vs, Trixie is visited by The Ghost of Hearts Warming Evemultiple years in a row, to the point that the ghost is forced to resort to showing Trixie the Ponyville of a world where she was never born, which looks exactly the same as the Ponyville from her world and asking her:
Ghost: Ok, so you say Trixie is the biggest thing to ever happen to Ponyville, right? Trixie: Without a doubt! Ghost: But in a world without Trixie Ponyville is no different. One minus zero is still one. Ponyville minus Trixie is still Ponyville. Do you understand what that means?
Tower of God: At the Name Hunt Station, Baam has to fight "Kaiser", who runs the place in an unending quest to make amends to her family, who showed her a lot of love until the point she failed their expectations and then abandoned her. Now, she lives by stealing the names of others and making them her servants or ransoming them off; the money goes to her family, who are deliberately not using it to pay off the debt that would free her. Baam asks her whether she remembers the names of the family she so fervently serves, and she replies that of course she does. Then he asks her whether she remembers her own name, and the realisation that she doesn't makes her see the absurdity of the whole thing.