Surprisingly enough, the beach/swimsuit episode had one near the end, Mikoto doesn't seem to enjoy herself very often due to being "embarrassed" of her "childish" tastes, When near the end she was having fun prancing in her frilly swimsuit it was kinda cute, almost made up for the squick the rest of the episode had. (Keyword being ALMOST)
There's also Misaka telling a physically worn down Kuroko that as her junior she can rely on her Onee-sama.
Uiharu being the only one to find Mitsuko's pet python Ekaterina-chan cute and petting her at the end of the episode.
"Erii, thank you for hearing my voice."
The end of episode 24, where Kiyama's students requisition a blimp to wish her happy birthday.
"We love you, Kiyama-sensei!! Get Well Soon!!
So many scenes involving Kiyama and her students counts as this.
Also in the manga, we get to see the Sisters arc from Mikoto's view. At the bridge scene, she's just realized none of what she's done has even slowed down the project at all, and has managed to convince herself that letting herself get killed is the only choice she has left. After all, its the real world, and there aren't heroes around to just fix everybody's problems. Then Touma walks up.
Mikoto:[thinking] I know how this looks. He must think I'm involved in the experiments. He must think I'm a monster. Mikoto:[out loud] I guess you found out, huh? You here to yell at me, call me a monster for letting these experiments continue? Touma: Isn't it obvious? I came here because I was worried about you.
Mikoto telling Accelerator that she's not working to stop the experiment out of jealousy, envy, vanity, or a desire for power; it's just that the clones are her sisters, and it's her job to protect them. The stunned look on 10032's face says it all.
Misaka 10032 explaining to some kids that Mikoto is the elder of the pair.
Touma calls Mikoto by her name for the first time.
A comment from Mitsuko finally convinces Mikoto to involve her friends in her adventures. She tells them about the Dark Side of Academy City... and they agree to join her without hesitation.
They don't even let her finish warning them about how dangerous it is before they start talking strategy, completely ignoring her warnings.
Episode 24 of Season 2. MISAKA 19090 explains to Shinobu why they're helping out:
"Those girls are using the same base program as us. In that regard, they're our little sisters. Do older sisters need a reason to help their little sisters?"
Also, 19090 (and by extension, all of the MISAKA network) to Shinobu: "Thank you for giving me a heart." Which shows that Shinobu's plan to give them free will did work, just not to the extent she'd hoped for.