Don't get us wrong, this cartoon is generally a happy one and does a great job of being positive. However, the show also does an excellent job of making us really feel for these candy-colored ponies. You really need the sad bits to make the happy bits richer after all.
When asked about Applejack's parents, Lauren Faust said that she did consider the idea of them being deceased. Of course, it was deemed too sad and other suggestions were made - ranging from them being salesponies to explorers. But since the subject has never been brought up in the show, it remains a mystery until the writers choose to define it. Until that day comes, fanon continues to run with the tragic stories in particular.
Applejack's hat is commonly believed to have been passed down from her late father, hence why she seems almost inseparable from it.
Even so, that hasn't stopped people from coming up with theories that make both origin stories true, like so.
Her stubbornness in Applebuck Season, where Applejack tried to harvest all of the apples alone without any help, is seen by some fans as her trying to live up to some standard she set herself between her parents passing away, and her taking on most of the responsibilities of the family business.
In Apple Family Reunion, it was confirmed by Senior Storyboard Artist Sibsy that the two shooting stars that appeared a couple of times in the episode were a nod to Applejack's parents. As it was said in-episode that the whole family was coming to the re-union, but we didn't see her parents at all, they could well be deceased, although it still isn't certain.
Fluttershy oozes woobie to such a degree that even PinkiePie avoids playing harmless pranks on her. In fact, the other 4 ponies have tried to be Cool Big Sisters towards her, despite being around the same age (and at least older then Pinkie).
It doesn't really help that while most of the Mane 6 are known for their strengths (Be it athletic ability, amazing talents or winning personality), she's mostly known for her weaknesses. They usually play up the "shy" part of her personality a lot. In the Discord two-parter, she admits herself that she's weak and is glad that her friends point out her flaws. If she was being sincere, she seems to have a very low opinion of herself. Even The Hub labels her as "The Misfit" in their commercials.
"Hurricane Fluttershy" seems absolutely dedicated to turning Fluttershy into a woobie, what with the flashbacks to her time at flight camp and her inability to fly nearly as fast as the other pegasi helping with the tornado. It also gives her one heck of a happy ending.
Adding to the effect, this is the only episode where we see Fluttershy actually cry. Not goofy cartoony Ocular Gushers or quiet sniveling. Full-on tears streaming down her face crying.
Ironically, though, if you think about it, Pinkie Pie actually qualifies as a Woobie just as much as Fluttershy, maybe even moreso, she just doesn't act it. Think about it: On the surface, Pinkie is a fun-loving Genki Girl who loves to throw parties. But as someepisodes show us, she actually comes off as something of a Stepford Smiler and she throws parties as a way of validation- and she thinks that if nobody likes her parties, then nobody likes her. This alone caused her to famously and completely lose it for a short while during "Party of One". Not to mention, grew up on a Rock farm. In her own words, "There was no talking. There was no smiling. There were only rocks." And then there's how viciously Discorddealt with her. And her breaking down in Berserker Tears in 'Baby Cakes' because of the twins antics and how desperately she wanted to prove she could handle the responsibility of looking after them. (Look at her hurt and offended reaction when Twilight tells her to her face she didn't think Pinkie could handle it.) Her desperation to get Cranky to accept her friendship also called into question why Pinkie Pie wants so many friends. And then in "Too Many Pinkie Pies", she's so desperate to make her friends happy and spend time with them, she clones herself and it all blows up in her face. And in "Wonderbolt Academy", she's convinced Rainbow Dash will have forgotten about her and the others, to the point where she has to go see Dash in Cloudsdale, although she seems resigned to the possibility that it's too late. Poor Pinkie Pie...
Although she sometimes seems more like a Jerkass Woobie, Rainbow Dash has woobieish elements when you consider her talent: Winning. Winning is everything to Rainbow Dash and she almost has a breakdown in "The Sonic Rainboom" when she's scared of failing in front of her friends and The Wonderbolts. The amount of fear/desperation she demonstrates during times where she does badly at something (Has a temporary Heroic BSOD in "The Mysterious Mare Do-Well", is scared of her friends mocking her over something she loves in "Read It And Weep", wants to beat the record in "Hurricane Fluttershy" to impress Spitfire and can't) makes you wonder just how low is Rainbow's self-worth that she thinks she absolutely must be the best or she's an unlovable loser? Not to mention, neither Dash or Fluttershy are shown to have any family so far...
In Wonderbolt Academy she desperately tries to please Spitfire, being crushed when Spitfire chose Lightning Dust over her as a leader. It turns out Lightning Dust doesn't give a crap about the other recruits and would do whatever it takes to become a Wonderbolt. This causes Rainbow Dash to give into peer pressure and help Lightning Dust make a tornado nearly killing Rainbow Dash's friends. When Spitfire finds out about this, she is enraged and gives Rainbow Dash the team leader insignia. Rainbow Dash definitely needs a lot of hugging especially having a sort of Ron the Death Eater status among certain fans.
There's also her disturbing tendency to be the victim in fanfics... at least two come to mind. If you know them, you'll really want to give her a hug.
Her crushed expression when Cloudsdale, her home town doesn't host the Equestrian games is heart wrenching. This becomes a Crowning Moment of Heartwarming when Ms. Harshwhinny gave her the rights to coach the young fillies to help with the Equestria Games. She's actually able to do something for the Equestria Games this time around!
How many times has Rainbow Dash had her hopes and dreams dashed (literally) before her eyes? And what happened to her mother? We get to see her father in an episode, but where's her mother? Is she still alive?
When she's not the victim, Rainbow Dash tends to have Ron the Death Eater status in which her flaws are amplified and her positive traits are removed turning her into a straight up Jerkass or even a serial killer in one fanfic. There's also art and fanfiction of Rainbow Dash suffering or being murdered. With all the crap fans put her through, she definitely needs hugging. There's also Scootabuse to consider, which sounded funny to some at first until you realize it's Rainbow Dash being put through Ron the Death Eater status. There's fanart and fics of Rainbow Dash physically and mentally abusing Scootaloo making resentment of Rainbow Dash run high among some people. It also hurts Scootaloo, which is something Rainbow Dash would not allow. And then there are some fans who actually wish she'd be killed off permanently.
Let's not forget, she's been excluded more than any other pony of the Mane 6 (like May the Best Pet Win!)and sometimes other ponies unintentionally make it sound like they're trying to exclude her. To elaborate, she wasn't invited to the Pony Pet Playdate, which all her other friends were there simply because she didn't have a pet. Then again in Daring Don't when she's not invited to a party because she's reading Daring Do. Imagine being close friends with someone and not being invited to a party because your friends thought you were busy. If you've ever been excluded from anything, you can really sympathize with Dash.
In a few episodes we can figure out that her bravado is simply a facade (meaning she's been putting on a brave face this entire time) and she's really a very insecure pony. In Castle Mane-ia she's just as easily spooked as the other ponies. Most of her brashness and arrogance is really just a Jerkass Fašade and she's really a sweet and caring individual underneath it all. If you can figure that out, she's far more huggable than she was before. A few of her focus episodes (most infamously The Mysterious Mare Do Well) focus on her flaws and shortcomings. And she's also the only pony who stood up for Fluttershy back in Flight Camp. You have to wonder if she's been holding back the tears this whole time. Imagine being a friend of an unpopular girl. And to drive the point home, you're the only friend of this unpopular girl. Imagine having to deal with your peers making fun of this unpopular girl but not having enough authority to stop it. That's how Rainbow Dash probably felt when she stood up for Fluttershy. Rainbow Dash is a total Woobie, she just doesn't act like one.
When Daring Do rejects her help, she seems broken. Especially when her trying to help supposedly got her captured. Daring Do herself is very similar to Rainbow Dash before character development and without The Power of Friendship. To meet the pony you've been idolizing ever since you got into books and having her reject your friendship is heart-wrenching. She does, however, form a sort of friendship with Daring Do/A.K Yearling in the end and even becomes her sidekick in the new book which she gets a week before everyone else, including fellow fan Twilight Sparkle. And according to synopsises from The Hub she's become something of a Reasonable Authority Figure in that she herself is given the opportunity to coach the young ponies to hold Ponyville's flag in the Equestria Games. Sure enough, she's matured enough to be a Reasonable Authority Figure and helps get Scootaloo out of a rut.
Here's another thing to consider: The reason Rainbow Dash sympathizes with ponies being teased is probably because she herself was teased as a filly, as proven by bullies calling her "Rainbow Crash" in Sonic Rainboom, possibly giving her PTSD. It's quite possible her aggressive tendencies could very well be the result of a mental disorder, especially since in the beginning she couldn't tolerate Fluttershy possibly because she didn't understand. This could lead one to assume Rainbow Dash's social skills aren't very good and she doesn't pick up on social cues the way a normal pony would. It's quite possible she may have some sort of social disorder which would explain her difficulty understanding certain emotions in certain episodes. Her friends usually have to tell her when something's wrong for her to say anything. And another thing, some fans call her lazy when her job is one of the most important: to ensure the weather matches the schedule which entails clearing and moving clouds. Those afternoon naps that she takes? They could very well be because of being totally overworked. The micro series comics play with this, and make Rainbow Dash go through a Heroic BSOD when she can't clear the clouds. The poor girl really works hard and without the admiration of the citizens of Ponyville, she's just a Broken Bird. You can really sympathize with her if you are a hard worker, similar to Rarity below.
Rarity is kinda a woobie as well when you think about it. She puts so much effort on her work in the boutique and gets little appreciation most of the time. Suited For Success, and Sweet Elite definitely proved it. While she may seem prissy and a bit prim, she has the element of generosity for a reason. Not only that but despite her overdramatic breakdowns and difficult to understand at times, it's fairly easy to relate to many people whom work hard.
Rarity's woobie status is cranked up in the Nightmare arc of the comics. She has bad self-esteem issues, and is afraid that her friends will abandon and forget about her once they find somepony kinder or more talented than her. The Nightmare Forces end up taking advantage of these fears in order to take over Rarity's body and make her the new Nightmare Moon. Needless to say, the real Rarity doesn't enjoy being the arc's main villain.
Rarity becomes a borderline example of something a Jerkass Woobie in Rarity Takes Manehatten being insensitive of her friends feelings, and yet being extremely generous to everypony. Her generosity ends up almost being her downfall in Manehatten when Suri Polomare copies her design and tells her she didn't win. After realizing what she put her friends through, causing them to miss the play they all wanted to see (yes even Rainbow Dash) it becomes too much for her to bear and she runs to the street in tears only to be confronted by her friends who say that it doesn't matter that she didn't win. Then it's revealed by Coco Pomell that she did win. Feeling better, Rarity takes her friends to a special showing of the play they wanted to see.
"Lesson Zero" implies that Twilight Sparkle was regularly teased in school as a filly, invoking this interpretation for some fans.
Even outside fan interpretation, she has a high order case of Super OCD, and (at least once literally) drives herself crazy trying to make everything perfect and appease her self dictated high standards, terrified of losing the approval of her peers and friends, especially Princess Celestia.
From her reputation as a bookworm and model student, her asocial behavior early in the series, her casual comments to Spike in the first episode that show she doesn't see any value in making friends, and her intense fear of failure in "Lesson Zero", it isn't hard to infer that before she came to Ponyville, Twilight didn't have any friends outside of Celestia, and her dedication to being a good student could be either the cause or effect of that. Either way, in "Lesson Zero" she's clearly freaking out at losing the friends she's come to value and being forced to give up her new and improved lifestyle to go back to being that asocial bookworm, this time knowing exactly how lonely and isolated she'll be now that she's had friends and has lost them because of her "slip-ups".
Spike is this to a lot of fans. Especially when he and Twilight Sparkle are like family to other each other. The reason of his woobie status is that one of his worst fears is no longer being Twilight's assistant and he often tries to help out whenever he can. Episodes like Owls Well That Ends Well and The Crystal Empire Part 2 proves that Spike cares about Twilight Sparkle very much.
Even if he isn't considered a woobie at the moment, he definitely has woobie in his future as due to his elongated lifespan, he will in all likelyhood outlive Twilight and all of her friends (including one he has a crush on) by a long way, excluding the apparently immortal alicorns.
However, since Twilight is an alicorn now, one potential source of angst may now have been eliminated.
Although that's kinda a vague description to go on. Some believe that they were playing with the words, considering that Celestia Luna and Spike are her friends too, Twilight wont outlive them. Think about it, why would an alicorn die? She holds an element that is too important to Equestria. Or the others (including spike) become immortal too.
Spike generally de-evolving from Butt Monkey to Chew Toy to No Respect Guy and possibly even Cosmic Playthingdefinitely puts him on this list. Considering that he actually had to put a picture of himself on top of another photograph of the Mane Six to make himself feel included in the picture, and the fact that he wasn't able to come to Twilight's birthday in "Sweet And Elite", became a monster that almost destroyed Ponyville on his own birthday in "Secret Of My Excess", and also was the only one who wasn't invited back to the Crystal Empire after he basically saved it from King Sombra (although it's soon made evident that there were understandable reasons as to why he wasn't invited) and he essentially rivals Fluttershy for top woobie in the show.
Here's a thing to consider: Spike is pretty much an outsider in a lot of respects. Not only is he the only male character in a group of females (not that unusual), but he's the only dragon in a society of mostly ponies. A society that barely knows just what is considered normal for a dragon. At best he's probably treated as a page boy or servant and at worst he's an exotic pet. It also doesn't help that it is in his nature as a dragon to become a greedy destructive monster. This is made worse when he actually meets other dragons and has a bad experience with them due to his upbringing, making him an outsider to his own kind as well. This gives the implication that while ponies appear to be inherently good by just being themselves, in order to "fit in" with what he knows, he has to fight against his natural instincts to get to the same level of "good". So it's very easy to feel bad for him when he's left out of things.
Power Ponies starts as pretty much a big "The Reason You Suck" Speech to poor Spike. When the ponies tell him they don't need his help, Spike feels left out and starts reading his comic book. When the ponies enter the comic and become the Power Ponies, Spike becomes Humdrum, the sidekick of the Power Ponies who can't do anything right and only gets in the way. Everyone gets captured and he blames himself for it. However, Spike is able to help Fluttershy save the day and the mane six tell him that he ''is'' needed, even if it's not all the time.
In Simple Ways, the mare he's liked since the beginning has a major crush on somepony else. And yet he still helps her, because he wants her to be happy.
The Cutiemark Crusaders
Apple Bloom also qualifies as a woobie. To elaborate, before she made friends with the Cutie Mark Crusaders, she was led to believe that she was the only one without a cutie mark, right after Twist got hers. It's also implied that Diamond Tiara and Silver Spoon just love bullying her rather than bullying ponies with "blank flanks." Plus, in the episode "The Cutie Pox," she desperately wanted to earn her cutie mark so badly, she steals the "Heart's Desire" plant from Zecora to get one, without thinking of the possible consequences. All goes well until she ends up having the cutie pox and she is unable to stop performing her talents. She then confesses to what she did to Zecora and ends up as a blank flank again. Poor, poor Apple Bloom....
Look at the above woobie section for Applejack. These also apply for Apple Bloom as well, only she may have been too young to really know her parents.
In some ways, Scootaloo can be seen as this, even without fan-interpretations. Within the show, Scootaloo has never been seen legitimately flying, and can only manage to hover above the ground while dragging her hooves at best. This is probably why she has a crazy obsession with Rainbow Dash, who is arguably the best flier in Equestria, to the point that she'd be her personal servant if it meant spending time with her.
This video claims that during the 2012 Brony Con, Lauren Faust said that Scootaloo was originally planned to be a character with a disabilty, and that an idea for an episode centered around Scootaloo involved the pony learning to accept that she cannot fly. While it hasn't been confirmed nor denied by Lauren Faust, leaving it's validity in the air, it has served as further fuel to the fan-theories that place Scootaloo in Woobie territory.
Another thing that makes her a target for easy Woobie-dom is the fact that unlike Apple Bloom and Sweetie Belle, she isn't related to any of the Mane 6, nor does she have any known relatives or seem to live anywhere in particular. Rainbow Dash and Fluttershy don't have any known relatives either, but Scootaloo is only a child. Naturally, fans have come to the conclusion that she's an orphan, homeless or both. To add insult to injury, there was a time when the trend of "Scootabuse" (fanart or fanfiction of Scootaloo being abused in some way, most often by Rainbow Dash) was popular. This plus the inability to fly gave rise to "Scootalove" (Fanart or fanfiction of Scootaloo being loved by somepony, most often Rainbow Dash).
Now that the episode is out, she definitely went through hell in it. First, she wanted to impress Rainbow Dash by flying in her performance. As expected, she doesn't fly, and ends up changing the entire routine till its all about her flying, which causes Apple Bloom and Sweetie Belle to get annoyed with her and end up leaving her at the train station. Scootaloo, with tears in her eyes, tears down the posters of her idol and other ponies she admires and throws them (along with her scooter) in the trash. Then Rainbow Dash comes in and reminds her to Be Herself and not focus on what Rainbow Dash can do. This results in Rainbow Dash affectionately rubbing Scootaloo's head and taking off for the Crystal Empire where the Crusaders are crowned the winners of the competition.
Sweetie Belle, especially in Sisterhooves Social. All she wanted was to help her sister out...
Babs Seed. Just look at her face when her blank flank is brought up and how she pathetically covers it with her tail, and it's easy to see why she chose to hang with the bullies.
Discord of all characters becomes one in the episode Keep Calm And Flutter On. He's both genuinely suprised when Fluttershy admits that she says that they're friends and then is hurt when she gets angry and denies that same friendship later after she was tricked. Just his saddened reaction alone is enough to make you want to hug him (And this is the same character that did absolutely horrible things to the Mane Cast).
Despite thenumerousatrocities he committed in his first appearance, the revelation that he's never had a single friend prior to Fluttershy, makes it pretty hard not feel sympathy for him, especially considering that he's likely gone more than a few centuries without one. It makes you wonder if his lack of companionship took a toll on his sanity and lead him to becoming the being we saw prior to Fluttershy reaching out to him.
After the events of "Boast Busters", Trixie's career and life were ruined due to her becoming a laughingstock throughout Equestria. She turns into a Woobie, Destroyer of Worlds due to becoming bitter as a result and obtaining an Artifact of Doom that corrupts her mind to try and carry out her revenge.
Princess Mi Amore Cadenza aka Cadance from the two-parter episode "A Canterlot Wedding". Imagine being taken prisoner on your wedding day by someone who you see taking your own form.
Worse than simply that: she was kidnapped in imprisoned alone in some forgotten mines without food or water while a shape-shifter takes her form and intends to marry her beloved so she can drain all his love for her. Even after being rescued, she has to find her way to the surface in despair (albeit with Twilight's help), witness her husband-to-be brainwashed, her aunt defeated in combat, and her home city invaded. She really has to go through a lot before she has her happy day.
If you look closely during the scene when she banishes Luna to the moon-a sad, heart-breaking scene in itself thanks to the voice acting-she's actually crying.
There's also Princess Luna, who, alongside Derpy Hooves, is one of the most popular characters despite appearing for only a few seconds in one episode of the entire first season. Fans jumped on the fact that the reason she went crazy and turned into Nightmare Moon was because she just wanted friends due to the fact that everyone was asleep at nighttime and she felt unappreciated. Until season two rolled around, one of the most popular interpretations of her was a traumatized filly who needed lots and lots of hugs and forgiveness. When she finally returned in "Luna Eclipsed," she was desperately trying to make up for her previous actions and convince everypony that she really wasn't evil anymore, but she was still afarcry from the sad little Shrinking VioletFanon had thought she was.
Still needs hugs, though. Her delivery may have serve to hide it a bit from modern viewers during that episode, but when she simply tried to address the other ponies in what is (to her) a perfectly normal, friendly fashion, consider what the other ponies' reactions to her must have looked like from Luna's perspective.
Supporting & Other Characters
Cranky Doodle Donkey is this in retrospect. Having spent most of his life wandering in search of his love, whose fate he never knew, he eventually gives up in his old age to live out the rest of his days with his distant memories. The moment he arrives in town, he gets harassed by an unwanted Pinkie Pie, briefly blinded, loses his wig, gets publicly embarrassed for his baldness, and then loses the most precious book he has to the pony who inflicted all this on him. And then he gets relentlessly chased all over Equestria and driven to paranoia by the same pony after he thought he'd thrown her out, to the point where he boards up his house and yells at her to go away. If it hadn't been for the contrived happy ending, that episode would have been incredibly sour.
Tank the tortoise. He just wanted to be loved...
Admit it, you cheered loudly when Rainbow Dash picked him!
Angel Bunny could qualify simply from his treatment from the fans. There's art of Fluttershy physically and mentally abusing him to her flat out abandoning him in middle of nowhere. And we're supposed to root for Fluttershy. That's not all though, despite his redeeming qualities, fans often ignore them and make him even worse possibly bordering on Moral Event Horizon treatment of Fluttershy. We haven't been told Angel's backstory yet, but it's possible he was an abused bunny who was rescued by Fluttershy or a rabbit who lost his family. While he's certainly not the nicest rabbit out there, he does not deserve he treatment he gets from fans. It's been shown several times that Angel really does care about Fluttershy, such as comforting her when she's suffering a Heroic BSOD, overseeing her personal training as her coach, and nuzzling her in later episodes. The first two examples happened almost right after physically abusing her and acting like a Spoiled Brat. Also, his well being is on the top of Fluttershy's priority list according to Castle Mane-ia where she almost bursts into tears at the thought of losing him. This is why she hesitates to let Spike look after him. You have to wonder what happened to the little guy to make Fluttershy so overprotective of him. Some fanfics (as well as the Micro Series comics) portray him in a positive light, having him comfort Fluttershy whenever she's down and serve as her personal secretary.
The Crystal Ponies in general. This is one those cases where an entire kingdom can be considered to be made out of Woobies. Their memories from before Sombra ruled are gone, leaving them with only memories of being his Slave Race under such awful conditions they're absolutely terrified of him. On top of that, they spend most of the episodes in a state of complete and utter depression due to what he did to them. Is it any wonder they didn't hesitate one second to blow him to kingdom-come? Oh, and they're now a thousand years behind the rest of Equestria.
The fandom's surprisingly dark intepretations of exactly how Sombra tormented them will make you want to comfort them even more.
Soarin', as of Rainbow Falls, the fan favourite lovable adorkable goofball of the Wonderbolts becomes this after he injures his wing while flying. None of the other Wonderbolts go to check on the guy, and lie about his injuries. It's because of him that Rainbow Dash makes the decision to stay with the Ponyville team.
Cheese Sandwich (yep, the character who is literally a pony version of Weird Al and happens to also be voiced by him) counts as one after his backstory is revealed. He was painfully shy and presumably teased much like Fluttershy as a colt, and he was very depressed as a kid, meaning he probably suffered from depression. It was only until Pinkie threw a party in Ponyville that he started to become the energetic pony he is today. He's also a traveller and his only companion is a rubber chicken, meaning he hasn't made many friends until the Mane Six.