Happens with Pinkie Pie and Rainbow Dash so many times it's easy to lose count, jokes about the latter's rainbow-coloured mane aside.
"Griffon the Brush Off" plays exactly like Pinkie Pie trying to vie for Rainbow Dash's attention after someone who seems to be her old flame shows up. This includes Gilda (see below) violently preventing Pinkie from intruding on her time with Rainbow, and Twilight outright stating she thinks Pinkie is jealous of Rainbow and Gilda's relationship. And at the end, after Gilda reveals herself to be a total bitch, Rainbow reaffirms that she'd much rather be with Pinkie. It even starts with something very closely resembling Pepe le Pew chasing Penelope Pussycat, complete with Pinkie doing his little love hop. Netflix's description of the episode doesn't help, saying that Pinkie becomes a "third wheel" between Gilda and Rainbow.
Pinkie's Rainbow Dash obsession is revisited in later episodes; it's almost a running gag that she's Rainbow Dash's Stalker Without A Crushwith similar themes to a stalker with a lesbian crush, with Pinkie affectionately calling her "Dashie" (something almost nopony else does), following her damn near everywhere (particularly in "Over a Barrel" and "Party of One"), and having a severe case of No Sense of Personal Space even by Pinkie standards.
In "Party of One" the pony sent to fetch Pinkie for her surprise party is Rainbow Dash. There's a brief scene showing Rainbow Dash's face framed in the heart on Pinkie's door, which was quite possibly the closest thing the show did to a real Ship Tease in Season 1.
Rainbow Dash tries to force Pinkie Pie to move by shoving her forehead in Pinkie Pie's butt. Pinkie then sits on Dash's face and Rainbow Dash says they'll have to do it "the hard way".
Rainbow Dash is willing to be far more patient with Pinkie's antics than she normally would be for other characters, even as she states she just wants to relax while Pinkie is being her usual self. In response to this, Pinkie actually goes quiet, something she almost never does unless things are serious.
Rainbow Dash and Fluttershy, Childhood Friends for longer than any of the other mane six members have even known each other, are frequently shown to be very close.
"The Super Speedy Cider Squeezy 6000" opens with Rainbow Dash barging into Fluttershy's room and pulling the blanket off of her as she lies in bed, causing the latter to blush and cover her chest (albeit rather pointlessly).
Rainbow Dash deciding to cut Fluttershy in on her deal to hoard cider (over all her other friends) says a bit.
"Sonic Rainboom" opens with Fluttershy recapping "the elements of a good cheer" that Rainbow Dash has been teaching her: "loss of control", "screaming and hollering", and "passion". It's given out of context with no explanation until afterwards, so it kinda sounds like she and Rainbow Dash are talking about... something else.
Rainbow herself at one point tells a distraught Fluttershy "But I need you!" while dramatic, emotional music plays. Then, after Fluttershy runs off, Rainbow Dash reaches out with her hoof, her disappointment and frustration mimicking a lover being disappointed in their other half.
"Dragon Quest" opens (what is it with these two and episode openings?) with Rainbow Dash and Twilight Sparkle trying to get Fluttershy to go see the dragon migration, when Rainbow Dash mentions when she and Fluttershy went to go see the butterfly migration together. Casual outing between friends, or really boring date? On top of that, Dashie has a picture of them on the migration trip together that she has been carrying around. Photo to remember the date, perhaps?
During the attack of the changelings in "A Canterlot Wedding - Part 2", Rainbow Dash almost kisses Fluttershy on the nose when helping her up. What sells this is that Fluttershy briefly closes her eyes as though she expected to be kissed.
It should be noted that there is a very brief swooshing sound effect during this scene, played at the EXACT SAME TIME Rainbow Dash is helping Fluttershy up. The problem is that it sounds almost exactly like a kiss in the exact spot where it could be very easily mistaken for a kiss. Yeesh.
Their first meeting (as shown in "The Cutie Mark Chronicles") is straight out of a Rescue Romance, with Rainbow rushing in to protect Fluttershy from the bullies tormenting her, and Rainbow herself saying that she was "defending Fluttershy's honour".
"Fall Weather Friends" might as well have been called "Belligerent Sexual Tension: The Episode", with the two going to ever greater lengths to best the other and prove their superiority. Even the lesson at the end wasn't that they were constantly competing, but them taking it too seriously was threatening their relationship, and the episode ends with them galloping off into the sunset together.
In "Bridle Gossip", Applejack fashions a crude set of bit-and-reins and rides an upside-down flying Dashie around.
In "Dragon Quest" all the girls are viewing the dragons together, and like the others Rainbow Dash is gazing up in awe at the them, when she suddenly glances at Applejack with a sly grin on her face and scoffs. "Pretty lame move! Is that all they got?" And then the dragon tries to set her on fire.
In "The Last Roundup", Rainbow Dash is depicted as the one pony closest to Applejack, including being the first one to notice when she's lying, and tackling her at the end of the chase scene, with a briefly triumphant expression.
Our heroine, in her unending quest for friendship, can get very close to the ponies around her.
As pictured above, in "Lesson Zero", Twilight Sparkle asks Rainbow Dash not to "hide her feelings" by cupping her face with both forehooves in a manner that could be interpreted romantically when taken in combination with her words.
Near the end of the episode Pinkie Pie nuzzles Twilight, the only pony to do so. (Twilight also nuzzled Applejack and Rainbow Dash respectively in "Dragonshy" and "Over a Barrel".)
Rainbow Dash:(to the pets) Alright, now these games will determine which one of you has the most important qualities I'm looking for in a pet. Speed, agility, guts, style. Coolness. Awesomeness. And radicalness.
Twilight Sparkle: Aren't those all the same thing?
Rainbow Dash: You would think that, Twilight. And that's why you would never qualify to be my pet.
"The Ticket Master" has Rainbow hovering by Twilight when asking about the ticket along with this line:
Twilight: Rainbow Dash! Were you following me?
Rainbow Dash: Yes-I mean no-I mean, maybe!
Despite "Hurricane Fluttershy" focusing primarily on Fluttershy and Rainbow Dash, Twilight and Dash exchange plenty of moments together including Dash's wings appearing to frame Twilight's face, the two seemingly hugging one another after whispering about Fluttershy's performance, and Rainbow Dash grabs Twilight's face close to hers when wanting to perform the hurricane again, complete with Twilight showing such concern.
In "A Canterlot Wedding Part 2", Twilight asks Shining Armor how he managed to get Cadance to marry him. He says that he mentioned that if she did, she'd get an "awesome sister". So Cadance married a guy just to get closer to his sister?
In the previous episode, Twilight's first reaction to reuniting with the fake Cadance is to wiggle her rump in her face. Later, the real Cadance returns the favour, although the actual wiggling occurs off-screen. (Sure, It Makes Sense in Context, but wow.)
Twilight is intensely reverent of Princess Celestia, well beyond even the usual level of grovelling obedience most ponies display towards her, and is utterly terrified of disappointing her or seeming "unworthy" in any way (as shown in "Swarm of the Century", "Bird in the Hoof", and especially"Lesson Zero").
In her flashback in "The Cutie Mark Chronicles", Twilight says that Celestia raising the sun was "the most amazing, most wonderful thing [she's] ever seen," and was the inspiration for her to pursue both magic and research as passions.
"The Crystal Empire - Part 2" shows that Twilight's worst, deepest fear is Celestia rejecting her and no longer being able to be her student.
Even when Twilight is transformed into princess alicorn, she is upset at first, because she thinks she won't be Celestia's student anymore. Awwww... or yikes, because that borders on codependency.
In "Luna Eclipsed", Twilight lures Pinkie into a dark alley with candy, and when she's out of view of the crowd she jams her against a wall with a hoof to her mouth and tells her "No shrieking. No screaming or squealing either." Twilight then shows Pinkie she isn't alone, at which point Pinkie flees in terror, prompting Twilight to tackle her and pin her to the ground. *
Context? What's that?
At the very end of "The Crystal Empire - Part 2", Rarity winds up holding Twilight's hoof.
Trixie and Twilight have amazing Foe Yay in "Magic Duel", and by the end of the episode they manage to become friends.
Twilight Sparkle: I can't stop thinking about Trixie!
Rarity: Oh, I just so wish it [the crystalization] was permanent! Did you see how my mane just absolutely sparkled?
Applejack: But, good things are better when they're a "rarity" (winks).
Rarity: Awwwwwww (giggles).
Applejack can be seen sitting with Rarity, comforting her after being forced to wear a tacky dress in "Magic Duel".
The micro series comics aren't free of examples either. The Rarity issue shows Rarity going on vacation... and bringing along a picture of Applejack to put on her nightstand.
Fluttershy and Rarity are shown to be very close even amongst the Mane Six in "Green Isn't Your Color", and Rarity seems more upset and jealous about Fluttershy's career forcing her to miss a (for lack of a better word) date with Rarity than even Fluttershy accidentally becoming part of the fashion spotlight instead of her.
Both parts of "The Crystal Empire" have a lot of these moments involving Rarity. There's at least one scene were it looks like she and Applejack are making eyes at each other, another where it looks like she's attempting to kiss Rainbow Dash, the aforementioned hoof-holding scene with Twilight, as well as a few frames where it looks like she's kissing Twilight.
The start of "Sweet And Elite" features Rarity profusely kissing Princess Celestia's hooves, thanking her for everything. For her part Celestia looks highly uncomfortable with the affection... while nervously glancing between Rarity and her bed.
Lyra Heartstrings with Sweetie Drops/Bon Bon
Sweetie Drops/Bon Bon and Lyra Heartstrings, two background mares who appear together in many episodes, are widely assumed to be either best friends or a couple. Second season episodes include apparently deliberate nods to this phenomenon:
Wide shots of the town common early in "Hearts and Hooves Day" feature a number of pony pairs standing around. Lyra and Bon Bon are among these pairs, though there's another Bon Bon paired with Shoeshine.
During two scenes in "A Friend In Deed", when Pinkie and a bunch of background mares are hopping across the roofs of Ponyville, Lyra & Bon Bon are shown moving in perfect unison. They are the only ponies in those scenes who do so.
There's an often-forgotten moment from "Fall Weather Friends" in which fan-favorite background pony Derpy Hooves (before the animators started intentionally derping her eyes again) drops a rose, which Fluttershy just happens to catch. It's cute and open to... interpretation.
Fluttershy reaches near Even the Girls Want Her status in "Green Isn't Your Color". Rarity wants her to model for her in the first place because "nopony is going to have [Fluttershy's] elegance and poise". Twilight says that "on her own Fluttershy could never do something unattractive" (hence her plan to use magic and make her do something unattractive). Photo Finish spends almost her entire appearance fan-girling over Fluttershy ("Yes! Even her sneezes are graceful!"). And the main reason Fluttershy hates being a model is the hordes of mostly female fans that flock to her wherever she goes.
In "Hearts and Hooves Day", Twist gives her holiday card to a gray colt, and they hug. This visibly disappoints another filly (Tootsie Flute), who had been looking in their direction. Was that filly hoping to give her card to the colt, or to Twist? Meanwhile, yet another filly (Alula) gives her holiday card to Diamond Tiara, who seems surprised by this attention.
In "Hearth's Warming Eve", Princess Platinum seems very close to her assistant/advisor Clover the Clever. Just look at Clover's introduction:
Later, she tells Clover she doesn't mind it when Clover "stoops down" for her. Yes, she's talking about crossing a stream, but hiding implications behind stuff like this is prime Radar material, and the fact is that she then proceeds to ride Clover across said stream. On top of that, Clover is wearing a bridle, which just adds to the domination play.
After the leaders thaw out, the Pegasi and Earth ponies share hugs and high-fives. Platinum and Clover, however, nuzzle.
The same episode has Flitter and Cloudchaser give each other a pretty tender hug a few seconds later.
Gilda is basically a huge mass of Ho Yay directed at Rainbow Dash. She has the same raspy voice and passion for athleticism that leads so many fans to think Rainbow is a Lesbian Jock, coupled with an extreme level of jealousy that quickly turns violent when Pinkie tries to get anywhere near Rainbow. She thinks a series of relatively harmless pranks are deliberate attempts by Pinkie to drive her away so she can keep Rainbow for herself, but when Rainbow reveals she was the one who set up the pranks Gilda is furious, and demands that Rainbow choose between them now. When Rainbow doesn't choose her Gilda is visibly hurt, and leaves immediately after tossing out a half-hearted insult.
Scootaloo has major Hero Worship towards Rainbow Dash, frequently to an obsessive level ("I'll do whateveryou want!"), with "Sleepless in Ponyville" basically being "Scootaloo stresses out attempting to impress her crush." It's mostly justifiable by Scootaloo wanting Rainbow to be her big sister, but Apple Bloom and Sweetie Belle don't display anywhere near the level of awe and admiration for their sisters that Scootaloo does for Rainbow.
In "Keep Calm and Flutter On", Celestia has so much faith in Fluttershy's abilities she puts the entirety of Equestria at risk, confident she'll be able to induce a Heel Face Turn in Discord. One part of the scene even looks very much like wedding vows if taken out of context.
"Read It and Weep" opens with Rarity and Pinkie Pie swooning as they essentially watch the "dazzling" Rainbow Dash work out. Twilight soon joins them.
Outside show media
The Theme Tune Extended (included as a sing-along on the DVD The Friendship Express) has such wonderful character puns, sung from Twilight's perspective, such as "Once smitten, twice Fluttershy", "You are the Applejack of my eye", "A heart that shines so beautiful, a Rarity to come by", and perhaps best of all, "As easy as Pinkie Pie."
In Adventures in Ponyville, when the player's (female) pony talks to any of the Mane Six, they'll sometimes say "Pony up!" to her. Unlike everything else they say to her, the speech balloon used for "Pony up!" is lined with a couple of hearts, making it seem like the Mane Six are casually flirting with the player's pony.
The German magazine comicDer Stern der Winterträume, Scanlated as The Star of Winterdreams, endswith the Mane Six sleeping together by the fireplace. Rainbow Dash is on her side, turned towards Applejack.
Look closely at this box-art◊ of some of the new and upcoming toys. Yes, that is Dashie looking at Pinkie Pie while their faces are framed together in a heart symbol.