FlutterSpike Hints

This is a list of hints of an obvious relation between Fluttershy likes Spike. This is from the anime adaptation so it's not the original show.
Season 1
Friendship Is Magic Part 1
Like the original version Fluttershy snaps out of her shyness upon meeting Spike, although in the anime she has puppy dog eyes and is clearly blushing. After Spike reveals he's a talking dragon, Fluttershy becomes even more enthusiastic. As Twilight and Spike walk home after this, Fluttershy continues to follow Spike while smiling. When Twilight reaches her library, she fakes that Spike is sleepy so she can go away, but Fluttershy instead picks up Spike and attempts to put him to bed, only stopped by Twilight. Later, at the party in Twilight's library, Spike with a lampshade on his head tries to convince Twilight to ignore Nightmare Moon's troubles, only to be pulled back in by Fluttershy who asks him to dance.
Friendship Is Magic Part 2
Fluttershy is seen hugging Spike during the party Pinkie throws in celebration of Nightmare Moon's demise and return as Luna.
The Ticket Master
In a quite lovey-dovey manner, Fluttershy waves and greets Spike while cleaning Twilight's library. This would go on to be a recurring theme.
Griffon The Brush Off
Spike, in this version, is first seen helping Fluttershy with some ducks. After Glida roars at her, instead of running away, Fluttershy cries in Spike's shoulders as he glares at Glida.
Boast Busters
Fluttershy has her arm around Spike while watching Trixie's show.
Bridle Gossip
Fluttershy was cowering behind Spike as the song Pinkie sings about Zecora occurs.
Swarm Of The Century 
Fluttershy, in the beginning, states that parasprites are the second cutest thing she saw, with her stating to the camera that Spike is the first.
Fall Weather Friends
Like the original, Fluttershy looks very concerned for Spike when he crashes into a sign.
Feeling Pinkie Keen
This is the second episode in which Fluttershy says "Hi" to Spike flirtatiously. In this episode, it occurs after the frog falls on Twilight's face. Fluttershy's response to Spike's hug is also different in the anime version. She isn't confused, but is more surprised of the hug and blushes after, thanking him for it.
Stare Master
This version has Spike frozen in stone too. Fluttershy's reaction is a waterfall of tears.
A Dog And Pony Show
Fluttershy looks very concerned for Spike as he hyperventilates over the loss of Rarity. She also checks on Spike quite worriedly after the fall down the hole.
Over A Barrel
After Spike is annoyed by everyone waking him up, Twilight comments that he is huffy. Fluttershy then playfully says "Spike the huffy dragon" while blushing.
A Bird In The Hoof
After Twilight allows Fluttershy to join the party, the anime version includes a scene where the latter asks the former how Spike is doing. When Twilight says Spike has been doing great work and is being taken care of well, Fluttershy sighs in relief with a wide smile.
Owl's Well That Ends Well
Fluttershy was heavily gushing over Spike in the opening. Later, Fluttershy says Spike is grumpy because he probably wants a hug and prepares to do so, but is stopped by Twilight. 
The Best Night Ever
Spike is shown at what looks like a bar towards the end. Fluttershy, for the third time, excitedly greets Spike as the ponies enter.
Season 2
The Return Of Harmony Part 2
The anime version includes Fluttershy informed by Twilight she was discorded and starts apologizing to Spike. Spike accepts her apology and she lets out a heavy sigh of relief.
Lesson Zero
The anime version has Spike tag along for the picnic, and both he and Fluttershy start eating together. Fluttershy is seen blushing as this starts.
Luna Eclipsed
Again, the anime version has Twilight and Spike together at all times and when the duo and Luna go to Fluttershy's, she peeks out and greets Twilight and Spike, with her commenting on how sweet Spike looks in his costume, making Spike blush uncontrollably.
May The Best Pet Win!
The anime version of the song includes this line:
Fluttershy: They have the same cute factor as Spike.
Raindow Dash (spoken): Now's not the time, Fluttershy.
Secret Of My Excess
This is the fourth time and first in season two that Fluttershy greets Spike in a lovey-dovey way. Rarity is now in love with Spike and a lot of the episode has Fluttershy jealous over her. Rarity confirms that she doesn't mind Fluttershy liking him too in the end and even says they can both fawn over him. Fluttershy happily agrees and both go over to hug and kiss Spike. This episode of the anime confirms Spike has a second admirer.
Hearth's Warming Eve
Fluttershy suggests a decoration of Spike in a Santa suit. Rarity also agrees on that.
The Last Roundup
Fluttershy, after Pinkie and the girls chase down Applejack, after Pinkie declares that no one should break a Pinkie Promise, they encounter Applejack where Fluttershy says "You don't see Spike doing that stuff, huh?" leading to a "What?-What?" between her and Applejack.
The Super Speedy Cider Squeezy 6000
Fluttershy offers to share her cider with Spike, to which Spike accepts. By the episode's end, they are seen away from the rest of the group drinking a single mug of cider with two straws.
A Friend In Deed
The song has a scene of Fluttershy with Spike on her shoulders having fun. It occurs in the background of the first chorus.
Putting Your Hoof Down
The very beginning has Fluttershy singing to herself about Spike. The same thing happens when she enters the market.
Dragon Quest
When Spike arrives with cakes, Fluttershy greets Spike in a loving manner again (second in season two and fifth overall). Directly after, Spike is ridiculed by Applejack, Pinkie and Rainbow for wearing a pink apron. Fluttershy is very disgusted at their behavior, to the point of tearing up for him. When Rarity states Spike is cute when he walks off angrily, Fluttershy agrees with her.
Hurricane Fluttershy
After Fluttershy's hallucination of a bunch of eyes mocking her poor flying skills, she starts sobbing and huddles herself into Spike, who comforts her.
A Canterlot Wedding Part 1
Fluttershy is the first to notice Spike running to them and greets him for the sixth time. She is also always by his side in her appearances in this episode after.
A Canterlot Wedding Part 2
Fluttershy is seen in a photo with Spike offering soda via funnels.
Season 3
The Crystal Empire Part 2
Fluttershy can be seen praying for Spike to be OK when he starts falling from the Crystal Empire. A tear streaks down her face too.
Magic Duel
Fluttershy at the beginning was worried that her animal friends will be harmed by Twilight's trick for a celebration. She watches everything from behind Spike. A similar scene occurred at the celebration where Spike is seen cuddling Fluttershy who is again unsure how it will unfold, and has taken to jumping in Spike's arms to watch.
Wonderbolts Academy 
The opening scene has Fluttershy with Spike next to her. She playfully flirts with him.
Spike At Your Service
Spike, for the seventh time, is greeted greatly by Fluttershy, this time as she's walking by Spike early in the episode.
Just For Sidekicks
Fluttershy gives Spike a cute little hug when he agrees to look after Angel.
Games Ponies Play
Fluttershy wonders if Spike can handle taking care of everyone's pets in quite a worried tone, to which Twilight tells her to shrug it off.
Season 4
Princess Twilight Sparkle Part 1
As the vines engulf Fluttershy's cottage, Fluttershy screams out Spike's name in distress.
Castle Mane-ia
The anime version has Fluttershy and Spike together, while Rarity joins Twilight. Fluttershy, after touching the organ and letting a loud, scary note play, she flies off screaming Spike's name. The stone figure of Spike gets crushed, leading Fluttershy to believe that Spike is dead, crying out for him and trying to lift the pillar off. She squeezes him tight when she sees he's still alive. 
Power Ponies
Fluttershy greets Spike her usual way the eighth time overall. She's also genuinely nice to him when he feels like a worthless sidekick and tells him to stay confident.
Bats!
Even in her vampire form, she still remembers Spike being her love interest. Fluttershy blows a kiss to Spike. She does so in her vampire form before lunging at the characters. 
Rarity Takes Manehattan
While on the boat, Fluttershy is seen sleeping with Spike on a bunch of crates, hugging him like a stuffed toy.
Rainbow Falls
Spike is in the audience, at one point he's seen cheering for Fluttershy, making her blush heavily.
Simple Ways
Fluttershy greets him the ninth time overall. Spike is jealous over Rarity who is smitten by Trender Hoof. Fluttershy snaps him out of that by hugging him, making him smile.
Filli Vanilli
Fluttershy is driven to tears when Pinkie increases her stage fright. She dashes behind Spike sobbing. She also winks at Spike, who happens to be in the audience, during the finale performance.
It Ain't Easy Being Breezies
Spike falls from a tree, and Fluttershy manages to rescue him before he hits the ground. She sighs in relief again.
Trade Ya!
Fluttershy shows concern for Spike as he wallows over the next Power Ponies comic before she gets dragged away by Rainbow Dash.
Equestria Games
Fluttershy is welling up while listening to Spike having a negative reaction on himself.
Season 5
The Cutie Map Part 1
Fluttershy plans on going on a trip with Spike, the main characters leaving her behind in this version.
Castle Sweet Castle
Fluttershy states she made a special bed for Spike because "he deserves it".
Tanks For The Memories
The anime has the sound of Spike screaming heard as Fluttershy explains hibernation to Rainbow. Fluttershy quickly finishes her statement before dashing off to help Spike. 
Slice Of Life
The anime version has Twilight mention who their favorite character is.
Twilight: Princess Celestia
Pinkie Pie: Cheese Sandwich
Rainbow Dash: Daring Do
Applejack: Big McIntosh
Rarity: Spike
Fluttershy: Spike as well
Party Pooped
Fluttershy greets Spike for the tenth time. She also reads a secret of his which is not revealed to viewers, though her reaction is blushing and giggling suggestively.
Do Princesses Dream Of Magic Sheep?
Fluttershy frequently cuddles Spike as she sleeps.
The One Where Pinkie Pie Knows
One of the questions Fluttershy asks to Pinkie as the latter is delivering cakes is if Spike is doing fine. Pinkie dashes off saying "Yes!!" quickly. The Pegasus sees him walking by and sighs with relief.
Scare Master
Whenever Spike is around Fluttershy, she would be blushing heavily. Also, when she was Flutterbat, she licked Spike's cheek with a wink before ripping his costume's fake head off.
What About Discord?
Fluttershy greets Spike for the eleventh time overall and poses at him.
The Hooffields And McColts
At the end, Fluttershy dreamily thinks of Spike as everyone looks on.