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 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".
Throughout most of the episode, Pinkie acts extremely oblivious to Dash's annoyance at not being able to get any cider, and while gushing about the cider she just drank, Pinkie leans further and further onto Rainbow Dash, until she's literally draped over Dash's back.
In "The Crystal Empire - Part 1", Rainbow Dash makes an ironic remark towards Twilight, and nudges Pinkie, as the two stand very close together. Pinkie takes the joke literally and seems to desperately try to gain Dash's approval.
Twilight: I LOVE research papers!
Rainbow Dash: Yeah, who doesn't?
Pinkie Pie: Oh oh oh! Lemme guess! Is it Spike? No no, Fluttershy? Rarity?
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.
In "Daring Don't", Pinkie hugs Dash and rubs up against her for far longer than is strictly necessary, before Dash pushes her away.
Pinkie Pie is infuriated when she thinks Rainbow Dash has been hurt in "Rainbow Falls", and threatens payback on who/whatever hurt Dash. In the episode, she also acts as the Ponyville Team's single cheerleader, and loudly cheers on Dash as she flies the relay race.
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 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. Fluttershy's breakdowns themselves seemed to be a combination of self-doubt and being upset for disappointing Rainbow.
Throughout the episode, Rainbow was oftentimes making intimate physical contact with Fluttershy. Hugging her, bringing a foreleg around her shoulders, touching her cheek, holding her at arm's length, and even sharing the equivalent of a high five.
Fluttershy showing up at the site of the reservoir during Tornado Day, just to give Rainbow moral support. Despite that she felt terrible and didn't even want to participate in the slightest, she still showed up to support her.
Rainbow almost immediately turns the praise to Fluttershy when Spitfire was congratulating her, even going as far as referring to Fluttershy as her "number one flyer". It's a Crowning Moment of Heartwarming for so many reasons and really shows how much Rainbow cares about Fluttershy.
"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?
Even if someone were to argue with "She kept it to have evidence so Fluttershy would owe her", that wouldn't quite add up. Why would Fluttershy need a reminder of something she'd not only remember being at, but had wanted to go to in the first place? It comes off more like a cover-up for the real reason she kept the photo, as commemoration.
While probably unintentional, Rainbow's line of vision in that photo is actually directed right at Fluttershy's cutie mark. So she actually was watching butterflies, just not the ones passing in the air.
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.
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".
In "The Crystal Empire - Part 2", Rainbow Dash actively seeks out Fluttershy to joust with her, likely just to spend time with her. Fluttershy asks her why she didn't ask somepony else to joust with her; Rainbow didn't answer that, but did agree to go easy on her when Fluttershy pouted.
"Keep Calm and Flutter On" not only has Rainbow acting more like a jealous and overprotective girlfriend when she sees Fluttershy being nice to Discord, but Fluttershy also called her "Dashie", something she never did before.
"Daring Don't" has yet another opening with the two. An excited Rainbow Dash was almost constantly touching Fluttershy in some manner, right to holding her hooves.
There was a bit going on between them in "Rainbow Falls", such as Fluttershy (along with Bulk Biceps) being part of Rainbow's three-pony pegasi relay team, and saying she was competing for Rainbow (and Ponyville, as well).
The sweet moments were many, but one in particular was Fluttershy's understanding and compassion Rainbow's goals. It was very touching to see how Fluttershy wasn't taking it personally and would support her no matter what.
Fluttershy and Rainbow Dash had an amazing amount in Trade Ya, its hard to pin down one scene pretty much every scene with the two dripped with Les Yay.
"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 "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.
Not even their human counterparts are immune. When compared to the other girls post-break-up, the way Applejack talks about Rainbow Dash makes her sound like a bitter ex-girlfriend. The two are also the only ones to apologize to each other on-screen and they even seal it with a hug.
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!
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.)
And then in "Three's a Crowd", Twilight makes quite a big deal over how happy she is that she and Cadance will get to spend time together, and how frustrated she is that Discord tries to get between them.
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 an alicorn princess in "Magical Mystery Cure", she is upset at first, because she thinks she won't be Celestia's student anymore.
At the end of "Feeling Pinkie Keen" the two of them are holding their hoofs together while they're reconciling.
Pinkie and Twilight get a bit at the end of Trade Ya when Pinkie reminds Twilight of the sentimental value of the books she's trying to get rid of.
Twilight: ...And this is the book I got on the day I met you.
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. note 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!
During "Dragonshy" Applejack saves Twilight's life from an avalanche and gets a neat little nuzzle in return for her heroics.
Applejack and Rarity both hate it when the other isn't themselves in "Simple Ways", and they both mention how much they know each other.
Rarity: (speaking to Applejack) ...You probably know me better than I know myself.
Applejack and Rarity spend the whole day in Trade Ya arguing over a trade each one wants, but will take all their collected items to trade, but instead of trying to convince the other that their item is more important they instead argue that the other should go get their item. in the end neither get their wanted item and instead trade half their stash to get an item similar to what the other wanted.
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.
"Filli Vanilli" also shows Fluttershy and Rarity giving an adorable nuzzle.
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.
In the first episode, "Mare in the Moon", Rarity drags Twilight to her house to forcibly dress her in several dresses, and starts gushing over her after learning she's from Canterlot, and gets really close to her cheek to cheek saying their going to be "the best of friends".
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.
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.
Since the ponies are also portraying the characters in a play, this could be considered another Rarity/Twilight moment.
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.
Since "The Mysterious Mare Do Well", she's literally fangirling over Rainbow Dash whenever she has a chance to be with her. When Dash was wavering a flag as a demonstration in "Flight to the Finish", Scootaloo watched with sparkles in her eyes. And once we see Scoots' house, guess which pony she has multiple posters of?
"The Mysterious Mare-Do-Well" begins with a meeting of the Rainbow Dash Fan Club, with the first order of business being coming up with a word to properly describe Rainbow Dash's awesomeness ("awesome" just isn't good enough.) Naturally, Scoots is the leader of said fan club.
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.
She's not that optimistic, though - she does make sure the Mane Six are all present and wearing the Elements of Harmony before de-stone-ifying Discord.
"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.
In "Daring Don't" Rainbow Dash violates Daring Do's personal space quite often◊.
In "Twilight Time", when the crowd of fillies start snapping photos of the CMC with Twilight, Scootaloo starts posing, including pulling Sweetie Belle to her side like they're a celebrity couple.
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.