iThink They Kissed. While loopy from laughing gas at the dentist's, Sam tells Carly she's a "pretty, blurry girl". She toys with Carly's hair a lot, then tried to kiss Carly and only Carly's quick reactions stopped it happening.
iSpeed Date. Sam (in a schoolgirl attire) handcuffs Carly to a chair and gags her with duct tape...
Sam: [about Carly] Who wouldn't want to go out with this?
There's no guys at the school that don't make Sam sick.
iQuit iCarly is a visual metaphor of divorcing parents.
In iSaved Your Life, Carly (while wearing a bunny suit) gives Sam a full, spread-legged, police style pat down that ends with a playful slap on the butt. This actually aired. On Nickelodeon.
After Sam is giving Freddie a hard time for his new relationship with Carly. Freddie asks her point blank if she was jealous of him. Dan Schneider even discussed that possibility on his blog.
Sam says that while not educated, she's a lot of fun. Carly confirms it and eagerly headlocks the blonde in a noogie and Sam is quite enjoying it.
In the extended version, after Carly admits that she's dating Freddie and locks herself in her room, Sam wants to talk to her. Carly pulls Sam into the room with her and closes the door. It's... ambiguous, at the very least.
The entire episode iFight Shelby Marx is so Les Yay filled, it spawned the fandom pairing Shelby/Carly.
Carly says Shelby is cute and mentions her butt way too many times. This quote sums the whole episode:
Carly: Your butt hasn't done anything to me, and I'm sure it's super-cute!
Sam removing Carly's robe.
iWas a Pageant Girl. Sam stripping the gown from Carly (as well as pulling her legs to take off her shoes) from her adjacent stall.
Carly: (mockingly) Thanks for being gentle! Sam: Ta-da! (emerges fully dressed) I feel hot! Carly: (annoyed) I feel violated.
Sam tells Carly (rather excitedly) that she looks hot in the pageant dress.
The entire pageant proper had Carly behave like a very proud mom towards her "daughter" as Sam takes the stage. Specifically during the introductory segment when Sam comes up she tells a pageant mother "that one's mine".
Carly and Freddie's reactions to Mrs. Ackerman's red dress are nearly identical, with Carly being more composed about it.
In iEnrage Gibby, Carly is awestruck when she sees Tasha. This exchange then follows:
Sam: Heh, I told you she was hot. Carly: Well, yeah, but you didn't say she was that hot!
In iCarly Awards, Carly tells Freddie that he's standing too close. She has no objections when Sam is literally pressed up against her, despite plenty of room to spare.
iScream on Halloween: after hiding inside a closet (where there was no shortage of personal space)...
Sam: Wait, whose butt is this? Carly: Sam!
Carly's tone of voice doesn't seem to be saying "Sam, don't touch my butt" so much as "Sam, don't touch my butt while we're on the air."
In iPsycho, Nora leans on her female classmate (played by Daniella Monet) and kisses her on her lips.
The camera angle makes it look like she kissed her lips but it was actually a dangerously close to mouth kiss on the cheek. But it's still a kiss, Nora could have kissed a boy but she just goes and kisses a girl. The girl's surprise is proof enough that the Les Yay was intentional.
In iSam's Mom, Sam decided to "make nice" with her mom, the woman she's been arguing with the entire episode and whom inflicts a Hilariously Abusive Childhood on her, just for Carly.
In iGet Pranky, Sam was in a deep sleep when Carly tosses a pillow against her face. Sam is wholly aware that it was Carly who threw the pillow, but instead of targeting Carly, Sam gives Freddie the blame and knocks him off with the pillow instead. This just blatantly proves that Sam will never dare hit OR hurt Carly.
In iLost My Mind, Carly licks Sam's hand. Granted, Sam was covering her mouth so she wouldn't tell Freddie something but why would licking her hand make Sam stop?
In iGo One Direction, Sam cheers when somebody mentions San Francisco (a city known for, among other things, being very gay-friendly), calling it her city, then claims she's never been there. Shortly after, she lays Carly's head on her shoulder and strokes her hair, calling her sweet.
Although they only met each other for part of a crossover TV-movie some of the interaction between Tori and Carly can come across as flirtatious.
Carly's line in iOMG that "(Sam)'s just a little awkward about liking guys" makes it sound like Sam is more familiar with liking girls.
In iBattle Chip Carly sniffs Sam's breath in the most intimate way possible, nearly sticking her lower face into Sam's open mouth.
Freddie declares that he isn't giving Spencer a sponge bath while he watches television. Not after last time.
Spencer's hypnotic stare session with Freddie in iWill Date Freddie
In "iRue The Day", when Spencer is showing an autographed message on his back, part of the message points to and compliments his back mole. Freddie touches it and says "That is a nice mole".
In iWas A Pageant Girl, Freddie and Spencer seem more interested in each other than in their dates. They even ignore an offer to make out with the two very attractive girls.
iBelieve in Bigfoot, when the cast is looking for Bigfoot, and they spot two boys:
Sam: They're not even cute.
The whole Gibby/Spencer massage scene in "iParty With Victorious".