Pretty much any scene with Kuroko that, in some way, involves Mikoto.
From Episode 2:
Postman: We have an order for Ms. Shirai Kuroko. Mikoto: What's the contents? Postman: Computer parts. Kuroko:[aside to audience] Phew, thank goodness these companies are always discreet about their products. Mikoto: Who sent it? Postman:Love Potions and Aphrodisiacs Incorporated. Kuroko: Why the hell did they bother to label it "computer parts" then!!
Episode 3 has several very funny bits: The reveal of what the villain has been doing to the girls she is attacking ("I have photographs, but it's not pretty. If you're going to look, prepare yourself."), the villain attempting to use the stun-gun on Mikoto, and the villain's Motive Rant.
Saten: Uh...what? Mikoto: Yeah, you lost me somewhere in the middle there.
From Episode 4:
Anything that involves Mikoto and Touma. His reaction to being told the score will be settled when Mikoto wins, her coming at him with a chainsaw made of vibrating iron sand, her reaction to trying to shock him directly (through his right hand), his hilariously bad attempt to give up, and the fact that she then proceeded to chase him around for the entire night.
Saten: This is a true story about what happened to an upperclassman's friend's boyfriend. One humid night when he passed a deserted park, he was asked directions to the station by a woman who was loitering around. As he was kindly explaining the way to her, looking somewhat distraught, she raised her arms...and suddenly... Mikoto: ...suddenly? Saten: ....took of her blouse. Mikoto: There's nothing scary about that at all!
Kuroko's reaction to hearing that the curse of the Undressing Woman is infectious.
Kiyama: Ah, today was fun. And I also got the honor of doing the next episode preview. Maybe I should slowly undress. So next tim- Kuroko: Don't strip!
Kiyama: Ah, today was also fun. How about I strip for the preview... Now, next episode— Mikoto: Don't strip!! Wait, I'm going to kick your ass!
Uiharu feeling so happy and in ecstasy of experiencing her dream of what it's like to be a Tokiwadai student during the mid-summer festival... until Saten decides to wake her up back to reality by flipping her skirt!
Practically any scene where Saten flips her skirt is hilarious. One particular scene is in Episode 9, where Uiharu is standing around, noting that Saten is late. Only for Saten to flip her skirt from behind (in the least subtle manner imaginable) and announces loudly "Today's blue stripes huh?" It's all topped by Uiharu crying and waving her fists in the air.
Kuroko getting mad at Kiyama for undressing in public at the cafe. What makes it funny is that Kuroko is talking about herself on how "Women with skewed sexual interests" gets interested in seeing Kiyama's naked body. In the manga Saten also joins her saying that no women should show her panties. While Misaka and Uiharu looked on.
Kiyama undressing in public in general are crowning moments. The very first time it happens, people mistake Touma trying to get her to put her shirt back on for him taking it off; he runs away screaming "It's not what you think!"
During the cafe scene, Uiharu and Saten are told she's a brain specialist.
Saten: Is there something wrong with Shirai-san's brain?
Episode 13. The gang is modelling swimsuits in a holographic studio. Once they're done, Mikoto stays behind to try on the kiddy swimsuit she avoided before, and accidentally broadcasts everything on the giant billboard outside. Touma sees it and goes, "You Have Got to Be Kidding Me!"
Episode 3 of Railgun S. Mikoto getting smacked in the head with a binder and Kuroko glomping Mikoto's giant teddy bear because it smells like her. Also Saten's reaction to Eri finding a stack full of cash cards.
In Railgun S episode 4, Mikoto, after being led to believe that the Level 6 Shift was stopped, starts acting unnervingly cheerful, actually paying for her drink and not getting mad when Kuroko falls onto her chest. Kuroko is disturbed by this, so she tries to provoke Mikoto by telling her what kind of underwear she's wearing today. Mikoto instantly drops the facade and without hesitation shocks Kuroko.
Mikoto's interactions with 9982; the argument getting interrupted by the ice-cream truck man, and 9982 stealing Mikoto's ice cream, then narrating her Blatant Lies about not eating it and the narration of her talking Mikoto into getting them tea, then Mikoto putting the Gekoto badge on 9982 and the slap fight when she wanted it back.
Shokuhou: Don't start running with all your might... Mikoto: I thought I was only jogging.
Also in this chapter, Misaka and Shokuhou getting into an argument and Misaka pointing out Shokuhou's eyes.
Mikoto: And what's with your sparkling eyes? Do you think this is a shojo manga? Shokuhou: I was born this way! Weren't you ever taught not to make fun of other people's bodies?
At the beginning of the Daihaseisai, the managers are tasked with getting two of the Level 5's to introduce the games with a speech. Shokuhou agrees readily enough, but asking Accelerator, Kakine, and Mugino goes about as well as you'd expect, Misaka's unavailable, and nobody can find any information on #6, so in desperation they are forced to ask GunhaSogiita. He forgets the speech in the middle of it, so he decides to improvise and ends up doing a ridiculous speech in which he inserts the word Guts! everywhere he can.
In a Railgun omake chapter, the male researchers from the Level 6 Shift project need the clones as close to the original as possible, so they try to figure out what kind of panties Mikoto wears under her shorts. A request for Tree Diagram to calculate a simulation is immediately denied ("Don't use me for stupid things"), so they send in the Hound Dogs, a black-ops mercenary squad. They break into the Tokiwadai dorm in the middle of the day in full gear...and are immediately slaughtered by the dorm supervisor. Just as the researchers are declaring that they'll have to take to the field themselves, the female researchers reveal that they just went out and bought 20,000 pairs of cheap panties.
In one of the non-canon Railgun omake chapters, Mikoto is talking to a newly amnesiac Touma about their fights. However, the way she says it sounds like something else altogether ("Every night, you chase me around and do This and That!"). Touma comes to the horrified conclusion that he's been raping a middle-school girl on a regular basis...so he immediately asks her to marry him.
The entire cookies incident.
First, after Touma gets hosptialized, Mikoto goes to visit him and brings some fancy store-bought cookies as thanks for his help. Touma then remarks that he would have expected her to bring home-made cookies and insults her baking skills in the process, resulting in her blasting him with lighting.
Then Mikoto goes to Saten to bake homemade cookies, explaining that she can't use the dorm kitchen because of all the people who would wonder who she was baking them for
Saten then begins teasing Mikoto relentlessly about having a boyfriend, to her flustered denials
Finally, when Mikoto goes to give them to Touma, she meets him unexpectedly and starts blushing and stammering while trying to explain that she made the cookies as thanks, leading Touma to think she's talking about ants and says he'll leave her to her research assignment. He does not get the cookies.
Episode 17 of Railgun S.
Kuroko gets freaked out when Mitsuko buys mice to feed to her pet boa.
Kuroko and Frenda get into a childish argument about whether Mikoto or Mugino is the best, leading to the former two groping the latter two's breasts and getting beaten up.
Kuroko bought turtle blood due to its fabled aphrodisiac properties. Naturally, Mikoto fries her.
Saten enters full-on Troll mode with Misaka, latching on every opportunity to tease Misaka about the cookies she made for Touma.
Saten names an attack after Uiharu's panties. Uiharu is understandably upset.
Mikoto tries to end the episode the same way as the first season, by saying, "There's never a dull moment in Academy City." Her friends interrupt her to her great frustration.
Everyone: Not when you're around, Misaka/Oneesama Mikoto: Just what do you mean by that!?
Chapter 63: Touma and Gunha's reactions to each other effortlessly dispelling and deflecting Angel!Mikoto's beams and their thoughts.
Touma: He punched down the electricity? Gunha: He negated the electricity? Both: Who is this guy?
Touma's reaction to Gunha's idea of getting him close to Mikoto: Fastball Special!
Touma: No, what? Wait! Wait!!! Waitwaitwaitwaitwaitwaiiiii——aaaaaaaaaaaaaaahhhhhhhhhh!
Remember at the beginning of Index Volume 11 Touma mentioned he was forced to dance with Mikoto and was kicked by Kuroko? Chapter 71 explains how it happens. When Mikoto is away to buy drinks, Touma, by coincidence, meets up with Saten (whom he met in Chapter 58). When Mikoto returns, her awkwardness towards Touma goes unnoticed by Saten and Uiharu and the two come up with a plan to get Touma to dance with Mikoto. Saten would first ask Touma to dance with her (in return for lending him her lucky charm) and once he leaves, she feigns an injury and ask Mikoto to take her place. Mikoto tries to come up with an excuse until she finally give in and drags Touma to the bonfire with her. During the entire time, Uiharu has to hold down Kuroko until she finally breaks free and drop kicks Touma, ending their dance.
Misaka first meeting 9982, whose first words are "Myah". Misaka is appropriately puzzled.
"Indian Poker" (Chapter 71.2) The nameless Ringlet Curl girl gives an Indian Poker to Mikoto in order to bond Mikoto and Misaki. As soon Mikoto uses it at night, she have a wonderful dream even commenting she likes it...that is until it shifted to her being Queen Misaki's maid. She finally snapped/wakes up when Misaki tells her to be her maid for the rest of her life waking up while Mikoto yelled "That's the last thing I want!!!". The best part is Kuroko tries to confess her love towards the sleeping Misaki and caught on the worst timing when she finish her confession and hearing Mikoto's line; shattering her dreams...again.
"Blau"(Chapter 72) It is hinted that Misaki has the same dream as Mikoto but in reverse.
Later Ringlet Curl Girl, who probably because of the slang under the "beeeep"-ed words completely missed why Mikoto and Misaki got so angry with "Blau", asks them whether they ever before dreamed about "a gentleman [they] like" in an effort to be conversational. The body language of their sheepish non-answers is priceless◊.
With New Testament 11 out, what makes this scene more hilarious is that they're both probably thinking of Touma.
Precog Boy: Shut up, you pervert! Uiharu told me to stay away from you because you're a pervert!
Kuroko:(Sitting on Uiharu's back) Did you really think you could outrun a teleporter?
Uiharu: I think we must always keep trying and never give up.
Immediately after, Uiharu (while still pined down by Kuroko) spends a page talking about how amazing it is that everything worked out fine and no one is seriously injured when suddenly Kuroko preforms a pro-wrestling move on her:
Kuroko: Yeah, it's really amazing (pulling Uiharu's head back) that you think you can escape by changing the subject like that!
The OVA consists of Mikoto being stalked by a mysterious feeling of always being watched and the others trying to track down the cause and finally resolving it. Then Uiharu begins praising Kuroko and in the process reveals that most of it was actually Kuroko teleport-stalking Mikoto.