Two words: Kio Asuno. At the tender age of thirteen, he becomes a Gundam pilot. Because he spent much of his childhood playing battle simulators under the watchful eye of his grandfather, however, he has no idea of the realities of the war he's entering into. His Wide-Eyed Idealist nature and Chronic Hero Syndrome causes him to undergo one of the most painful Trauma Conga Lines in entire Gundam franchise. To start, he takes lessons with his mentor Shanalua, who, as a war orphan who hates killing, is horrified by the poisonous beliefs Kio learned from his grandfather about the enemy. Later, he finds out that she is The Mole for Vagan, but believes that explaining about how she's a nice person to the crew would bring her back. Shanalua flatly refuses because she would be executed for treason and sacrifices herself when Vagan mobile suits attack. Not long after painfully losing his mentor, he finds out that his father is alive as the Captain of the Bisidian pirates. Even so, Flit tells his grandson to forget it ever happened and believe his father is still dead, sowing his gradual detachment from his grandfather.But the poor kid can't even rest then. In Episode 35, having barely avoided death from his sheer lack of experience, Kio gets caught into a Vagan trap while the Diva was en route to retrieve the EXA-DB. While he did escape an episode later, he saw his grandfather try to shake off the Vagans in his outdated AGE-1 and, due to his tendency to follow his heart than his orders, dives right back in to save his grandfather. What ensues is him being captured by Zanald and being brought to Second Moon. But what truly seals the deal are Episodes 37 and 38. Upon his arrival, he gets transferred to Lord Ezelcant's palace, if only because he resembles Ezelcant's dead son Romy. Even with his fairly luxurious imprisonment, Kio realizes that Vagans are forced to deal with rampant poverty and/or the traumatic and deadly diseases from Mars Ray exposure. This is brutally driven home when he is brought to Deen's house after being pickpocketed. Kio finds that Deen's sister Lu (who is a woobie in her own right) takes an immediate liking to him. Not long after a simple dinner, however, he also learns that she is terminally afflicted by the Mars Ray disease and that she wants nothing more than to have something remotely close to a normal life, such as going outside, in the little time she has left. Growing close to her, this realization triggers a Heroic BSoD. This causes him to bring the condition that he could receive medicine for Lu (even though it only relieves the symptoms and doesn't actually cure the disease) when Ezelcant asks him to unlock the AGE system's security protocols. Having grown attached to Lu and having won her brother's trust, Kio found happiness during his imprisonment in Vagan, so it seems like the kid's finally going to get a break, right? Nope. In the middle of his father's rescue attempt, Kio returns to Lu's house one more time to deliver more medicine. What he finds instead is her brother mourning her peaceful death and a diary of all the memories she could have had with Kio. And as he escapes Vagan in his damaged AGE-3, he breaks down and finally realizes that there are others in Vagan that are just like Lu.
Saji Crossroad His older sister is murdered (and may have been raped by her killer), his girlfriend is badly injured and later stops contacting him (and becomes a Dark Action Girl), and he inadvertantly leaks information that causes the deaths of many Cathara members. And to regain what he has lost and repair the damage he's done, he must go through Heaven and Hell and then back; namely by taking part in combat and fighting for the same organization he blames for what happened to him.
It's not hard to feel sorry for Allelujah after learning his backstory. Raised solely to fight, Allelujah has to abandon Marie in order to escape the colony to avoid termination. During his escape with fellow children designated to be killed, Al's Ax-CrazySplit Personality takes over and kills and eats his friends when food starts to run out. And then poor Al is forced by Hallelujah to pull the trigger and kill every child inside the facility when he returns with his Gundam, before finding out in the first season's finale that his archrival was Marie all along.
Soma Peires/ Marie Parfacy can be seen as one as well. Born through artificial scientific methods, Marie spent most, if not all, her childhood trapped in a glass container being constantly experimented on. In the process of making her telepathic, the HRL scientists stripped her senses of touch and sight, making her very lonely. Although the scientists let her bond closely with Allelujah, Marie eventually loses contact with her only friend as he has to escape to avoid termination. This makes her optimism and strong faith in God rather inspiring and ironic at the same time, as anyone else would surely be anything but optimistic or spiritual.
In terms of actual suffering, the pilots from Mobile Suit Gundam Wing are pretty hard to rank, but they all go through some tough stuff:
Quatre Winner's psychotic destructiveness after his home is blown up and the fact that it climaxed in his 'killing' his Practically Canon Love Interest put them pretty high on the woobie scale.
Duo Maxwell has it easiest during the actual series run, but his backstory makes him a woobie as well. He lived on the street from a very young age, but the gang he ran with died due to a plague, including his idol Solo. After he gets taken in by the Maxwell church, the church gets occupied by terrorists who demand a mobile suit or they'll kill everybody in the church, so Duo goes and steals a suit, only to find that the church was razed to the ground while he was gone. He took his nickname, "Shinigami" because everybody who got close to him died, and he gave himself his name from Solo and Father Maxwell from the Maxwell church, so he could never forget that he failed to save them.
While the protagonists of the Mobile Suit Gundam franchise seldom get off easy, usually as an illustration why it's a bad idea to put a teenager in the middle of a war zone, Victory Gundam stands out by going out of its way to make the lead character Uso's life a living hell. Forced to pilot the eponymous Gundam against his will by leaders who honestly only value him for his skill, Uso and the Gundam develop a repuation by the enemy as an unholy terror that needs to be destroyed as quickly as possible. Uso does not take it well. "Stay away! You won't be killed if you stay away!" quickly becomes his... er... battle cry".