Shirou: According to Father, "the old man's like a yakuza boss." Of course, this is just prejudice. He's not "like" a yakuza boss, he "is" a yakuza boss.
To go to the church covertly, Saber wears a giant yellow raincoat to blend in. Because a mustard raincoat twice her size is inconspicuous.
In Fate Hollow Ataraxia, this becomes a Brick Joke when Saber reveals she was kind of upset with Shirou about having to wear his raincoat.
Fate
During Fate, Taiga is slow to accept Saber's living in the Emiya household as (she thinks) a Pretty Freeloader who's out for Shirou, and so challenges her to a sword duel. While Taiga is a world-class kendo champion, Saber in her lifetime (if her class title is any indication) literally lived and died by the sword, and is good enough to disarm Taiga almost instantly. Taiga degenerates into sobs and "SOME STRANGER TOOK SHIROU AWAY...!"
While training in the dojo with Saber, have Shirou ask if she can teach him a 'super move that can beat a Servant in one shot'. The air immediately goes cold and dead, and Shirou gets one more reminder that a girl is scariest when she's smiling...
Ilya: You—- *executes 230-hit combo on Shirou*fuckin' chicken grill! I can't believe this! I can't believe anyone would be such an insane gamer that they'd come to this Tiger Dojo! Osu! You shouldn't be here! Beat that Goldie quickly and protect Saber or I'm going to get mad!
In Tiger Dojo 13, (after Saber kills Shirou), Taiga and Ilya are happy to finally be able to give useful advise on how to avoid the bad end... until Ilya points out that this dojo was so difficult to find that any players who came to it were probably trying to get there in the first place.
Taiga: Oh, this feels so good! I finally fulfilled my reason to exist!
Ilya: Yes, I can finally be proud of myself…! …Oh. But Taiga. Most people passed the Saber affection score check, right?
Taiga: Yeah, Shirou isn't the type to ignore Saber-chan. You normally wouldn't end up like this.
Ilya: …Taiga. Um, it's really hard to say this. But if it's that rare, wouldn't that mean not many people would come to this dojo…?
Taiga: Oh. I-It's probably all right. The skip function and the Tiger Stamps are intended just for this. Everyone will probably desperately play in strange ways to get to this dojo.
Ilya: ...Yeah. By that point, everyone will hate this bad end with its weird conditions. So in other words, your dojo that tries to make everyone happy is actually something that troubles players trying to fully complete the game.
Ilya: ...?! Man, explosion endings are the worst...!
Lancer, when he's about to face off with Gilgamesh because they decided to betray each other at the same time, Saber takes him aside to tell him his opponent's real identity. Lancer's reaction is to cross his arms and say something to the effect of "Well, shit. That's just my luck." Then he goes and fights him to the death anyway.
Early on, before Saber and Shirou have finished hammering out their living arrangements, Shirou gets called into school to deliver something to Taiga. Too nervous due to her presence to explain why he doesn't want a strange beautiful foreign girl following him to school, he just tells Saber to stay behind... and she refuses, and just wordlessly follows him. Eventually, after several more flustered orders, she says that unless she gets a real reason, she simply must assume it's not truly an order from her Master, and thus she cannot properly tell what he is saying. Yes, in case you're wondering, the ancient and dignified spirit of power and nobility did just excuse her disobedience with the equivalent of "Lalalalala, I can't hear you!"
When it's established that Rin is going to live at the Emiya house, though no one tells Taiga at first. Instead, she walks in that night, greets Shirou, greets Rin, goes into the kitchen...and does an honest-to-god delayedDouble Take lasting four seconds (and five sprite changes) before screaming.
"WAIT, WHY IS TOHSAKA HERE?!"
Saber's appetite is used for comedy gold again. There's a scene where Shirou asks her what kind of food she likes, and she proudly (and adorably) claims that she has no weaknesses when it comes to food as long as it is well-prepared. So Shirou asks her what the chefs in her life were like to make her like this... and the world turns gray, with Saber letting off a wave of killing intent as she remembers how sub-par the cooking was in her time. Seriously: Don't screw with the girl's food.
Shirou: ...! Let me down, you idiot! What the hell are you thinking?!
Archer: I don't know, just shut up, you idiot! I'll get a headache thinking about how stupid I am if you tell me about it!
Shirou: Idiot?! You know you're an idiot, and you still call me an idiot?! You idiot!
Archer: ...! Are you a kid or something?! You can't be helped if you're a kid and stupid! At least pick one, you idiot!
Shirou's inventive way to see if Issei is a Master. Just check for the command spell! By demanding he strip naked! In the middle of school! Subtle, Emiya.
Rin and Shirou are meeting up with Ilya, and have to pass through her boundary field. The field mildly shocks Shirou in acknowledgement. Then Rin tries to pass through it...
Shirou: "Oh. Be careful though. It'll shock you a bit."
Rin: "I know, I know. I can tell how bad it is by looking at you - UKYAAAAAAAAAAAAAAAAAA!!!
Shirou: "... I guess there's personal differences in the alarm. It was light in my case.
Rin (not listening): "That does it, kid!... I heard you laughing!..."
The scene when Lancer shows up and Rin and Shirou start arguing about who's supposed to fight and who's supposed to run away.
Rin: Hey, say something, you idiot...! T-this is as if we really do love each other...!
Lancer: Hey, it's not 'as if'. You two are already in love. Even I can tell, and I'm only watching it from the side. But she's actually denying it? This is troublesome, kid.
Shirou: ...Well. I already know Tohsaka's troublesome.
Lancer: Oh, how reassuring. Then I shall take care when I socialize with her. But she's fun to tease, so I'm going to entertain myself while we're together. You don't mind that condition, right?
Shirou: ...All right. We'll go with that. We'll have your help until we beat Caster.
Lancer: Then it's decided. Well, let's shake hands.
Rin: I'm so mad!!! Fine, I'm breaking my tie with you guys!!! I'm going to go beat Caster by myself!!!!
Heaven's Feel
The scene where Taiga reveals Sakura's bust size. She's an 85, E-cup, and acts all flustered about it.
Shirou's narration can be a goldmine of good moments. This is how he enters a restaurant:
And now I'm entering this terrible dungeon willingly. The manager will bring a menu as soon as he sees me. That'll be the end of it. At the very least, I'll have to order something that uses sweet vinegar. It'll turn out horrible if I order something like twice cooked pork, and mapo tofu is out of the question. That stuff is dangerous. It'll melt my tongue. I hear the judge of hell pulls out your tongue, so such awful food could easily come from there. The manager traveled abroad to train his cooking arts, so maybe he trained with the devils.
Kirei just seems to snark his way through Heaven's Feel. One of his best is after Rin and Shirou get schooled by the route's Big Bad and are literally deposited on his door step.
Kirei: I wanted to leave you two, since you made a rather ugly pair as abandoned children go, but you were also dead on your feet. Had I done nothing, there would have been two dead bodies in front of my church. A church cannot afford that image, so I had no choice but to treat you.
There's a serious scene where Rin and Shirou have a tense argument about whether to kill Sakura. Cue a sudden crashing sound, Rin and Shirou stop in their tracks... and Kirei, casually providing his own commentary in the background. Leading to this conversation:
Kirei: (with a serious frown) Running footsteps. The only ways out of here are through this chapel or the back door. What is she doing, breaking the window to go outside? (smiles) ...Oh, I see. Most windows here have fixed fittings. She had to break it to get out. For someone who's still recovering, she's pretty violent.
Rin: Recovering—- do you mean Sakura?!
Kirei: Who else? From the room she was in, you can somehow hear everything said in the chapel. I am sure she fled when she heard you discuss killing her.
During the dinner with Sakura and Rider, choose to say you like Rider. What follows is 2 minutes of Shirō digging himself deeper to avoid both Sakura's jealousy and Rider's irritation. The scene ends with the two of them saying "I'm waiting for your answer!"
The scene where Ilya and Rin begin randomly arguing over which of them is Shirou's 'owner'. And then you get to pick which one of them is. Rin's is kind of lackluster, but if you choose Ilya, both of them just completely freak out. Rin goes completely berserk and starts accusing Shirou of having an... 'ulterior motive' for his decision, while Ilya glomps onto Shirou in utter delight and promises to protect him from the 'scary old girl', which of course just makes things worse...
While rescuing Illya, Kotomine cheerfully makes Shirou free-climb Einzbern Castle, Shirou complaining the entire time. Then Kotomine jumping out the window with Illya, spurring Shirou to follow. By jumping out the window. From eighty feet up. He nearly breaks his legs, and Illya and Kotomine look at him like he's an idiot. His defense?
Shirou: Well, I was left behind, and since Kotomine jumped with Ilya, I thought I'd look bad if I didn't do it too——
