Akinari Kamiki from Persona 3 AKA the Dying Young Man social link. Suffering from a terminal illness, poor Akinari just has the strength to wait for you at the bench by the shrine every Sunday. He is so jaded from living in a world where he is destined to die that he suffers from depression, and uses reading and writing as an outlet. He writes a story about a bird and an alligator that starts out happy, then gets sadder and sadder. It has a happy ending as he finishes it just before dying, grateful that the main character was there to support him, and with a renewed feeling of hope in the world.
And among the main characters, there's Mitsuru, the ostensible leader of SEES. At first she seems to border on an Emotionless Girl, but once you learn about her tragic childhood, her underlying vulnerability and concern for everyone else, and as her current woes continue to pile up, she becomes more and more of a woobie character. Just try not to wish you could hug her whenever she strikes her sideways glancing, clutching one elbow and about to cry pose. Oh, and her dad was killed in front of her and there was nothing she could do to prevent it (she was being crucified that time)
Plus there's an offhand comment about her being "forced" into the whole situation with the Shadows and SEES, which doesn't help matters.
Fuuka and Ken as well. Fuuka is small, sickly, and frequently bullied. Her low self-esteem and obsession with pleasing people are implied to be the result of emotional abuse by her parents. Ken's mother was killed when Shinjiro lost control of his persona. Ken then dedicated his life to killing Shinjiro, with the intention to commit suicide afterwards. Junpei, who grew up with an alcoholic abusive father, falls in love with a girl who is one of the villains and later dies. Akihiko, an orphan who lost his sister in a fire years ago, causing him to become obsessed with power, thinking that he could protect anyone if he were strong enough. Then his best friend dies.
Most of SEES are woobies. Then the PSP remake comes out, and the female route woobifies the last guy you'd expect to be a woobie. Shinjiro Aragaki. While he puts strong front, he's a sentimental and tender guy who worries for others like a distant brother, and is willing to give up his life to fix his mistakes. In the social link he warms up to the heroine (whom he's hinted to have fallen for), and entrust her with protecting SEES. Now that's sweet and all but maxing it out leads to a not so happy conclusion. He goes in a coma, the SEES treat as if he died and move on, and when he does wake up, the girl he loves dies to become a seal. And he's dying too.He also has the distant sideways glance, and when you examine it closely, you realize he's crying. Ouch.
Ryoji Mochizuki. Befriends SEES and is a happy-go-lucky Handsome Lech. Then we discover he was brought into existence solely to bring about The Fall on the world that he has come to love thanks to being sealed inside of the Main Character. This forces him to fight his friends (and, in the case of the female protagonist, the girl he loves) in a battle he knows they can't win.
Ai Ebihara from Persona 4 goes through a remarkable transformation from Rich Bitch into this should you develop her Social Link far enough. At one point, she asks you to ask her secret crush who he likes; when he identifies your party's tomboyish Genki Girl as the object of his affections, Ai has a breakdown and tries to jump from the rooftop. Calm her down and you'll learn that her haughty attitude is the product of crushing self-esteem issues. She used to be a Gonk until her family came into some money: they moved out into the country and she reinvented herself, but her new attitude only managed to alienate people.
Hello? Naoki is this game's true woobie. As the brother of the first victim, Saki, as if his sister's death was not enough, his neighbors now shower him with unwanted pity, his friends are too sorry for him now to be as close to him, and people in general just treat him differently. Towards the end off the social link, Naoki even considers dropping out of school. It makes it worth maxing out the social link when he thanks the protagonist for hearing him out, and taking the time to hang out with him.
Really, a good percentage of the S.Links are good Woobie material. Hisano Kuroda, for example, feels guilty over her husband's death, because before he passed on, he got a crippling disease that afflicted him with amnesia. Thus, he forgot about Hisano every day despite her efforts to take care of him, and she felt the man she loved died the day he got that disease. The pain would make Hisano wish he would die sooner, and her wish was granted, turning her into the depressed and ashamed old woman who calls herself Death.
Yumi Ozawa, one of the two possible Sun Links. Her story starts out relatively light, then hits a Drama Bomb when her Disappeared Dad comes back into her life via hospitalization. As her mother drops everything to care for the man who abandoned them for another woman, Yumi is left to pull their household together and cope with her massive amounts of resentment at having to seemingly sacrifice everything for somebody who never seemed to give them a second thought before now. Then she winds up somewhat reconciling with him while he's on his deathbed, as he asks her to live up to her name and 'bear fruit' before passing away.
Yosuke is essentially Junpei with a bit more likability and Wobbie material. a guy who is bored with life in a small town. He is often picked on by other girls and is always on the Disproportionate Retribution side of Chie's rage as a result (from physical violence to humiliation). On a more serious side, he often viewed himself as inferior to the main character (Something Junpei never got a chance to voice to Minato in his lack of Social Links) and is the one most heavily hit by the murders as Saki's death gets to him the most when he finds Namatame and Adachi.
Hell, how about Namatame? His life was destroyed, his lover was murdered, and the murderer deceived him into thinking he could save the next victims when he was actually putting their lives at risk, framed for the murders he desperately wanted to prevent. When he learns the truth, he is utterly horrified and remorseful.
Nanako Dojima. Her mother died when she was very little, and her father has slowly grown more and more distant. She's forced to be very independant, and is very, very lonely. Later, she gets a "big bro" in the form of the protagonist, but as her SL progresses, you find out just how freakin' upset she is when she runs away from home at age seven, and then her father doesn't come to comfort her!! Things are finally looking up at the end of the SL, but then she gets kidnapped, becomes incredibly sick, and DIES. She only comes back if you don't kill Nametame, but she's ill for the rest of the game. The fact that she's one of the most adorable characters of the Shin Megami Tensei franchisedoes not help.
Naoto Shirogane's a gifted and famous detective brought in to help solve the murders in Inaba. The problem? Nobody on the force will take Naoto seriously, seeing Naoto as Just a Kid and getting in their way, something that Naoto is very much aware of and frustrated by to the point of desperation. And then there's the gender identity issues she's working through.
Teddie deserves a spot on the list for all that happens to him in the second half of the game, especially the Bad Ending paths. Not only does he have deeply burried existencial issues and gradually begin to question his right to exist in the human world and have fun with his friends to the point that Yosuke, of all people, regularly has to smack some sense into him so he doesn't just run off again, it also turns out that he's actually a Shadow born of the feeling of loneliness, who ended up becoming self-aware and discarding his monstrous form, a fact he remembers this fact upon seeing Nanako Dojima "die", which causes him to feel helpless and inconsequencial to the world. In the Bad Ending paths, Teddie returns to TV World, never to be found again, even if Nanako survives, most likely reverting to a mindless Shadow and thus, de-facto dying himself.
And Persona 3 and Persona 4 are both a flower-filled meadow in comparison to some of the stuff the Persona 2 cast goes through. That in itself is a pretty sad statement, but given the nature of Atlus's Mega Ten games... The biggest Woobie label goes to Tatsuya and Maya. That's right, the main characters. Why? Play through Innocent Sin, then play through Eternal Punishmentnote Especially for Tatsuya, he saw Maya killed moments after his victory against Nyarlathotep, and then Philemon said the only one way possible to reverse it is to sacrifice his memories with Eikichi, Lisa, Jun, and every other person he met in his journey to create a new world. As Eternal Punishment shows, Tatsuya ended up too scared to accept being left alone. To hammer it home, one of the ways to show how suffering he was in is that... he has the option to punch Philemon in the face for involving him with the latter's Xanatos Speed Chess with Nyarlathotep, as in saying "Why the hell did you put me through all this shit for your... speed chess!?" But that's not even going into some of the crap the other characters go through.
Maya is even getting a comfort-hug on the cover art of Eternal Punishment (by her Persona), and is crying on the manual cover.
Also in Eternal Punishment, you get to meet the very same Tatsuya from Innocent Sin and as the game progresses, you learn the shit he went through in the IS timeline. At one point, Maya, being the protagonist, had the option to just shut him up by giving him a Cooldown Hug because it's THAT bad. And it was aww-inducing.
And did you think the first game was all happy and sunny? Think... again...
Maki Sonomura/Mary. A bedridden girl forced to stay in the hospital near damn everytime with her mother constantly at work, which caused her to hate her mom. Then she's unwittingly used as an experiment which creates another world with herself being split to three, her ideal self joining you and is seemingly honky-dory and cheerful... and when she learns the truth, she's utterly broken and nearly lost her ideals.
Kei Nanjou/Nate Trinity is the snotty pragmatic guy who even suggests most of the sadistic choices. But when it comes to it, he's a shining example of Lonely Rich Kid with his butler Yamaoka/Alfred as his constant companion (and embarrasses the hell out of him). Said butler get killed VERY EARLY in the game and Nanjou witnessed his last moments tearfully, made one last promise to be the best there is and made him truly lonely. He's still a snotty jerk in the rest of the game, but a snotty jerk we can feel sorry for, and we know him being snotty and always aiming for the top is the promise he made for his only most treasured person.