Ten's Woobieness can actually be partly attributed to David Tennant's eyes. Those things are enormous. And beautiful, but we won't go into that.
Especially, especially in "Midnight," when he's immobilized by an Eldritch Abomination and is being forced to repeat everything it says. The way he manages to convey so much terror and anguish with his eyes alone makes that episode downright hard to watch. Of course, "Midnight" really deservesits own section here...
Hell, the Doctor's been a woobie from the start. Let's see: Forced to run from his own people, makes his granddaughter - the only family he has left - leave him so she can be happy (he tried to make it look like he was okay with it, in truth it was heartbreaking for him; note the awful moment in the very next episode, where he forgets that Susan has left), he places the people around him in danger, and despite his best efforts to keep them safe has failed in one of the biggest Tear Jerkers of all television, has tried time and again to bring out the innate goodness in all life and then ends up forced to kill once he realizes there's no other way, and has continually been forced to regenerate, which doesn't always end well...
And how can you forget the fact that he (or at least it's heavily implied) killed his own race?
People may call a lot of it out as Wangst, but really, Ten has the best reasons to cry at season finales. In series 2, he loses the chance to tell Rose that he loves her when they're about to be separated by a dimensional barrier forever (at least until the end of series 4 which greatly negates the woobie)...in series 3, his best friend-turned-nemesisdies in his arms... And then of course he gets a prophecy of his own death, the root of which turns out to be a lovely, sweet old man who Ten kind of wished was his dad earlier on.
The "former best friend dies in his arms" one gets even worse; the Master chose to die just to spite the Doctor. Just to make him feel the pain of being the last member of his species again.
Fandom-induced example: somebody on the Doctor Whomacro community ihasatardis took a photo from the filming of Matt Smith's first episode and gave it a woobie spin. Suddenly even the rabid Ten fangirls wanted to take Eleven home and feed him cookies.
Woobieness highlighted oh-so-badly (as in "Oh, god...*sniffle*") in "The Hungry Earth": The Doctor tries to save Amy from getting sucked into a hole in the ground, but fails. Oh, god, his expression says, "Don't leave!"
And all of this is just the emotional trauma. Throw in all the times he's been electrocuted, irradiated, exsanguinated, electrocuted, possessed, poisoned, Mind Raped, electrocuted, and otherwise subjected to physical agony, and the Woobieness reaches epic levels.
The interesting thing about Eleven is that he tries not to let himself be the Woobie too much of the time. "The Lodger" in particular shows him putting on a brave face. This probably makes him a Stoic Woobie.
It comes through even clearer later; not only does he face a situation that he knows will kill him three or four times (depending on how you count it), on the few occasions when events from his previous regenerations have come up, it's clear that he's still just as tormented by guilt as Ten was- he's just much better at hiding it.
In "Amy's Choice", the Doctor says "There's only one person who hates me as much as you do." but doesn't elaborate until later. Hint: it's himself.
And from "Day of the Doctor" the War Doctor takes his place as the woobiest of all his incarnations, due to how utterly broken by self loathing and sadness he has become because of all he has seen and what he will be forced to do to save what's left of the universe.
She'd been skirting woobiefication for a while, but Donna's mindwipe in "Journey's End" finally propelled her fully into this trope. In a way Donna might actually be a woobie from her first appearance, she has a horrible relationship with her mother, her shouting at everyone is a cover for her very low self esteem, and now she's in love and getting married... to a man who is poisoning her with the coffee he makes for her everyday (a gesture that probably touched her at the time), so she can be the chemical key to unlock the hatchery for a bunch of starving omnivorous spiders... She's always had it pretty bad when you think about it.
"All that attitude, all that lip, because all this time... you think you're not worth it." Poor Donna.
The end of "Journey's End" is especially sad when you take into that this episode was the first time we see her actually feel good about herself for once then her memories are ripped away from her.
A number of companions fit into the woobie category as well, Victoria and Nyssa being examples. (Deborah Watling, who played Victoria, has said as much in interviews.)
Sarah Jane Smith. She spends most of her time with the Doctor being beaten up, tied up, blinded, and otherwise abused, and the capstone is that when at the end of her time, instead of dropping her home in South Croydon, he leaves her in Scotland.
Fauxtastically shanghaied by a Well-Intentioned Extremist? Check. Possessed by Shelobus of Borg? Check. Made to hallucinate some of her worst fears by a military scientist seeking to facilitate the conquest of humanity? Check. Nearly turned into a psychotic Audrey II? Check.
Fans of Adric tend to see him as a woobie rather than The Scrappy; his parents died at some point before his first appearance note the show never elaborates on this, but the Expanded Universe and Word of God say it was a forest fire, then his brother was killed in front of him. He's constantly trying to prove himself to the Doctor only to be scolded when he messes up (and even sometimes when he doesn't; there's a moment in the Doctor Who Missing Adventures novel Cold Fusion where the Doctor ignores and then chides him for asking if he's okay after having a seizure), repeatedly fails to save people (including his mentor and his brother in his introductory story, which itself contains a bit of Reality Subtext since Matthew Waterhouse's own older brother had committed suicide just 2 years earlier), spends nearly all of Castrovalva being Mind Probed by the Master while desperately fighting to keep him from hurting his friends, pretty much everything that happens to him in "Kinda" (is left to his own devices by the Doctor, which included being a played-completely-straight Only Sane Man trapped in a research station with at least one Ax-Crazy and being assaulted by an entire native tribe intent on killing him while stuck in a transport robot that feeds off his brain waves) and then he dies alone thinking he'd just failed to save the world. Oh, and he was almost turned into a vampire. And when he was tired of being an outcast (see quotes below) and wanted to leave the TARDIS crew to go back to E-Space, the Doctor blew up and argued something to the extent of "you can never go home again."
The Doctor: What's the matter?
Adric: I'm fed up.
The Doctor: Why?
Adric: I'm tired of being considered a joke!
The Doctor: Oh, no one thinks that!
Adric: Then why am I constantly teased?
The Doctor: Well, everyone's teased from time to time!
Adric: Yeah, but not as often as me...
The Big Finish Doctor Who audio The Boy That Time Forgot, debatable canon aside, cranks it up quite a few notches, especially when we learn the true nature of how he survived Earthshock: The Doctor's subconscious guilt had taken over during block transfer computations, creating an alternate universe for the freighter to crash in harmlessly, leaving our young Alzarian all alone in a jungle world without humanoid contact for 500 years and eventually turning him into a crazed insect-king abomination in time obsessed with revenge and just wanted someone to love him again. Oh, Adric...
In the end, the worst part is ultimately the fact that you can't take Adric in your arms and tell him everything's going to be okay...because it won't be.
Rory's also a case of going from a Butt Monkey to a Woobie. The first time we see him, he's just Amy's (pathetic) male friend (the one the Doctor identifies as not being the "good-looking one"), who seems to be an Unlucky Childhood Friend, perpetually bound to come in second to the Doctor. Amy leaves him on her wedding night to go travel the universe with the Doctor. When they finally pick Rory up to go along with them, he ends up basically being the Butt Monkey for all of his first episode. By "Amy's Choice", though, we grow to see him more as a Woobie who barely believes his luck that he's the Victorious Childhood Friend and just wants things to be normal. By "Cold Blood", his woobie-fication is complete: he pulls a Heroic Sacrifice for the Doctor and dies telling Amy that she's beautiful. When he returns at the end of the series, Amy can't remember him, and just after she does, he accidentally kills her. Then he spends 1894 years guarding her body waiting until she comes Back from the Dead. And they've killed him again since. There's a tweet out there where a fan asked Moffat if he was going to kill Rory once every season.
Moffat: Once? JUST once??? Where's the fun in that?!
Amy herself hasn't had an easy time of it- abandoned by the Doctor as a child, growing up obsessed and thought to be mad with four psychiatrists, gets mind raped by an angel, gets dragged underground thinking she's going to be buried alive, fails to save van Gogh, has her boyfriend die in her arms before being erased from history, then she finds him apparently revived, and just after she manages to remember who he is, is shot and killed by him. To top it all off, her family got eaten by a crack in time before she ever met the Doctor.
No wonder Eleven/Amy/Rory has become such a popular One True Threesome in fandom. These 3 Woobies suffer so beautifully together.
Then there was "A Good Man Goes to War". Dear God, was she put through the wringer in that one. And just watch this prequel for "Let's Kill Hitler".
"The Girl Who Waited" and "The God Complex" make a near-perfect double whammy. After "The Girl Who Waited", you want to hug Rory and the two Amys. Not so much the Doctor, but don't worry, he's likely added it to the near-endless list of things he hates himself for. Then comes "The God Complex": The Doctor breaks Amy's faith in him, and breaks a part of himself too.
A Dalek as a Woobie? Tortured into near-insanity; alone in the universe of space and time; cut off from orders and companionship; forced to pollute itself to regain power; adapts to survive, in the process becoming "no longer pure Dalek". Cannot kill its enemies; admits fear and disgust at itself. Then is finally Driven to Suicide. "This is not life. This is sickness." A different set of values, but definitely a Woobie.
Let's talk about Rose for a sec, shall we? It's one thing to know that your dad's been dead since you were a baby, but suddenly being able to go back in time and save his life only to find out that he's supposed to die in order to keep the timeline stable and save the rest of that reality from being eaten by Clock Roaches? JESUS. On top of that, she later gets separated from the man she loves by a supposedly unbreakable barrier between dimensions, and nearly two seasons later when she finally crosses the universes to see him again, he's dead. "But I came all this way..." Luckily, she helped repair the timeline.
Also there's Martha, who only thinks of the Doctor but he never returns her affections. Her most woobie-tastic moment is probably when they land in the early 1910s and the Doctor becomes human. Martha's a servant and isn't treated well because she's black (or a Londoner, she jokingly claims) but doesn't leave the Doctor's side. She's then forced to watch him fall in love and says quietly "He had to go and fall in love with a human... and it wasn't me."
Not to mention Walking the Earth during "The Year That Never Was", needing to live in constant fear of The Master as she travels the planet constantly, telling people stories about the Doctor... who is being tortured aboard the Valiant, with her family also there being treated as The Master's slaves and her being aware of it all this time... Of course, by this point she's graduated to Iron Woobie due to her enduring courage and resilience.
Mickey Smith. In his first episode, "Rose", he is attacked and eaten by a rubbish bin and replaced by a plastic duplicate. After he is rescued by the Ninth Doctor (who is always mean and condescending to him) and escapes in the TARDIS, he is dumped in an alley with his girlfriend, Rose, and is clearly traumatized by the ordeal. The Doctor then offers Rose, and only Rose, the opportunity to travel with him, leaving Mickey alone and the last person to have seen Rose before she disappeared. Over the next year, Rose's family make his life a living hell, as they believe he murdered her and are quite public in voicing this opinion. As a result, he becomes a embittered recluse. When Rose returns in "Aliens of London", she does not see him to apologize, although she is able to convince him she is sorry and the two briefly reconcile. However she still acts like a jerk, getting angry with him seeing someone else even when in the last story she considered herself "available".
He even gets more pitiful in "Rise of the Cybermen"/"Age of Steel" 2-part episode, where we find out that his grandmother died, and he blames himself because she slipped on some loose carpet he was supposed to staple down. He also only gets to talk to the parallel world's version of his grandmother for a few minutes before he is kidnapped. Also during the second part, his counterpart, Ricky, dies, causing his allies, as well as Mickey himself again, to blame him for his death. Also at the end of the episode convinced that there is more purpose for him in the parallel world, stays behind, and the Doctor can't ever come back to get him.
Vincent van Gogh, from the Eleventh Doctor episode Vincent and the Doctor, does a pretty good job of solidifying himself as a Woobie even though he only appears in one episode. Everyone he knows hates/fears him for being insane, the villagers blame him for the deaths of the Krafayis's victims, he curls up on a bed crying when he learns Amy and the Doctor are leaving because they're the only people who have ever been really nice to him, he mentions, 'in passing', that children throw rocks at him because they're "frightened" of him, and when Amy and the Doctor refuse his parting gift of a painting (they think it's too valuable), he assumes it's because they hate it. This results in a Crowning Moment of Heartwarming when they take him to the present-day art gallery and show him that everyone will love his work.
The crowning moment gets partially dethroned to a Tear Jerker. Amy, fully aware of van Gogh's impending suicide, spends the episode dedicated to convincing him not to do so. She and the Doctor are so convinced they've succeeded, they rush back to the museum to see the "new" van Goghs... only for the museum to be exactly as they left it. Amy, having recently and unknowingly lost her One True Love, gets a Heroic BSOD as she realizes van Gogh still commits suicide, and she's saved only when the Doctor delivers his Aesop: "The way I see it, every life is a pile of good things and bad things. The good things don’t always soften the bad things, but vice versa the bad things don’t always spoil the good things and make them unimportant. And we definitely added to his pile of good things."
And then there's the reason he commits suicide: he has a vision of the TARDIS exploding, causing him to believe that the only two people who cared about him, who made a difference in his life, are dead. He dies without ever learning the truth.
Kingpin and Bellboy from The Greatest Show in the Galaxy. With Flowerchild, Juniper Berry, and Peace Pipe dead, they're the only ones left who resist the Gods of Ragnarok, and they've been all but destroyed themselves.
The K-1 Prototype from Robot. Forced by the Scientific Reform Society to go against its programming and violate the First Law of Robotics, then forced to kill the scientist who made it. Then, it absorbs an energy blast and grows to enormous height, and has to be destroyed. And all this time, only one person ever showed it kindness, a fact the Doctor lampshaded.
Katarina. Acolyte to a priestess who is a world-class bitch until her whole city is sacked, and then she goes more than five thousand years into the future into a world she cannot possibly understand. She is held hostage by a desperate criminal and ends up having to space herself and him to keep the Doctor from diverting from their mission.
Haroun, Maimuna, and Safiya from The Crusade:
Haroun: Last year my house was a fine and happy place. A gentle wife, a son who honoured and obeyed me, and two daughters who adorned whatever place they visited. Then El Akir came to Lydda and imposed his will. He desired my eldest daughter, Maimuna, but I refused him. Barbara: So he took her? Haroun: Yes. Well, when Safiya and I were away he came and burned my house. My wife and son were put to the sword.
Ace reaches this a few times in her last season, especially in Ghost Light when she tells the Doctor about how her best friend Manisha was killed by racist boys who firebombed her flat when she was 13.
And while the Remembrance of the Daleks novelization has Manisha and one other person in the family surviving and going to live with relatives elsewhere, it also has Ace getting flashbacks to the fire and the hospital room at any sign of racism.
That female slave in The Romans. Also Tigellinus. And super-woobiedom is likely in store for Tavius, as well.
The Game Station Controller. The poor woman was wired into a giant broadcasting satellite at the age of five, used as the WetwareCPU by the Daleks, but she turned out also to be an example of a Heroic Albino by defying them and helping the Doctor find out where they were.. Even so, she deserved a hug from having spent a life wired up to a broadcasting station that does nothing but broadcast Bad Futurerehashes of bad reality TV and game shows.
Lazlo, from "Daleks in Manhattan" and "Evolution of the Daleks". He's already working in a menial position during the Great Depression, but okay he's with a girl he's crazy about and who's crazy about him. He sees her off to her show, is hanging around her dressing room, and then he hears something in the props room. Cue later in the episode, when we find out that he was kidnapped on the Dalek's orders and because he wasn't sufficiently intelligent, they decided to turn him into one of their pig/human slaves. The good news is that he escaped before they could steal his mind. The bad news is that he now has a pig's face and spends his time hiding in the sewers and watching his girlfriend in secret because he doesn't want her to see him like that. Oh, and he's going to die soon, because the pig-slaves just don't live very long. The Doctor does manage to fix the dying thing, but he still has a pig's face, although the good people of Hooverville give him a place to stay.
Even some of the Monsters of the Week qualify. In addition to the aforementioned Dalek, there's the Ood in "Planet of the Ood" (lobotomized and sold as slaves), the Krafayis in "Vincent and the Doctor" (abandoned, wounded and blind, on an alien planet), or the Minotaur in "The God Complex" (kept imprisoned for god knows how long, and compelled against its will to feed on innocents even though all it wants to do is die).
The Master! Especially John Simm's Master. Okay, so he's an insane rogue Time Lord determined to take over the universe and make us all do horrible things, but he has issues! Especially in "The End of Time."
Jackson Lake in "The Next Doctor". First off, he found he is not in fact the Doctor - who he thought he was is one big lie. Why does he think he is the Doctor? Not just because of a Cyberman data base, no; he saw his wife get killed, and the trauma of it made him WANT to be the Doctor so he didn't have to face the pain. Don't worry, in the end it turned out okay. The Cybermen kidnapped his son and the Doctor saved said son. Now Jackson Lake can have a family with his son and Rosita.
Jamie plays the jumpy, overprotective, hopelessly loyal Team Normal (he's a piper) to two super-geniuses, which more than occasionally gets him treated as useless — and then his woobiness is cemented by his ultimate fate: he's subjected to Victory Guided Amnesia and sent home. To Scotland in 1745. The last we see of him, he's being shot at. The Expanded Universe mitigates this just a little - no telling of Jamie's future lets him die there.
River had a pretty awful childhood, to say the least. The rest of her life was spent watching the man she loved, along with her parents (who never got a chance to raise her), forget about her. Also, she died after having her worst fear come true and ends up trapped in a virtual world. As subjective as she is, it is hard to not feel a bit sorry for her.
Winlett and Keeler from The Seeds of Doom. Imagine being transformed into a crazy plant with a Utopia Justifies the Means instinct. And it's even worse for Keeler because his boss wanted to see what would happen.
Oswin Oswald from Asylum of the Daleks. Stuck in the Dalek Asylum for a year, she thinks she's trapped in an escape pod from a crashed ship when she's really a Dalek herself.
Captain Jack Harkness. he lives for millions of years, ends up as a giant face, his friends die on him, and the Master kills him painfully and repeatedly. Poor Jack.
At least two of his best friends. The Doctor and Martha, were at his side when he finally did die for good
Madeleine Issigri, and her father Dom as well, from The Space Pirates. Caven, the pirate leader, has long since coerced her into becoming an accomplice by the time of the story. Then it is revealed that he's had Dom imprisoned in his own mine since she was a little girl.
Autloch from The Aztecs. He has had serious qualms about Human Sacrifice as long as he's lived, but the other priests view it as vital. Then a Rule 63 reincarnation of Yetaxa shows up and vindicates him—no, Tlotoxl has unmasked her as a fake.
The Marshchild from Full Circle. It's a young Marshman that is terrified of the Doctor when it first encounters him, only to (foolishly) let its curiosity overcome its fear and follow the Time Lord, right onto the Starliner: a stranded spacecraft filled with humans that fear and hate its kind. If the sight of it cowering and whimpering when it finds itself surrounded by hostile humans isn't bad enough, there's a subsequent scene in which it's trussed up in a net, screeching and whimpering in terror; and then a scene of the Doctor attempting to protect and comfort it, at which point it starts making noises that sound disconcertingly like a cross between the grunts of a pig and the sobs of a baby. To make matters worse, despite the Doctor's attempts to save it, it ends up dying a horrible, pointless death in the laboratory of the Starliner's resident Mad Scientist, its last moments alive spent groping towards a video monitor on which it can see the face of the one person who showed it kindness: the Doctor.
Eighth in "The Night of the Doctor". He is so upset by the fact the Time Lords are becoming so hated a woman refuses to be saved by him that he would prefer to die with her. And he dies as he renounces the title of the Doctor. The story also makes his Big Finish adventures canon and considering all that he went through in them...
Eight in Big Finish Doctor Who out-does all the other Doctors on Woobieness, having one of the most horrible lives. He saves Charlotte Pollard then discovers her existence is destroying history. He tries to pull a Heroic Sacrifice to save her, then has his TARDIS turn on him for preferring to destroy her then killing Charley and saving history. Eighth then has to exile himself to a universe without time, which he says is like losing a limb. He finally returns but his companion C'rizz dies and Charley decides to leave him. Then she decides to stay... but due to amnesia the Doctor thinks she ran off upset at him. The ending of "The Girl who Never Was" easily outdoes "Doomsday".
The finale of "The New Eighth Doctor Adventures" easily outdoes New Who finale sadness. The Doctor's great-grandson Alex Campbell and Lucie Miller die defeating the Daleks and the Doctor leaves utterly broken.
The War Doctor, who spends his life rejecting his title and fighting the Time War, seeing untold suffering throughout space and time. He even wants to die as he destroys Gallifrey. And even though he ends up helping to save Gallifrey it will take centuries before the other Doctors acknowledge him, as they think of him as a Monster that destroyed his race. But then Eleven learns what really happened and vindicates the memory of his past life when he affectionately calls him "Captain Grumpy".
Ianto Jones is a very woobie character in the Whoniverse. Let's see...
Ianto's actor, Gareth David-Lloyd, stated in an interview that he believed that, in desperation to get and keep his job at Torchwood for Lisa's sake, his character had been getting it on with Capt. Jack since the beginning. After Lisa's death he just sort of never stopped sleeping with Jack because he needed something to hold onto. Which makes a heck of a lot more sense then Ianto just randomly hooking up with Jack a few episodes after his GF was murdered by his friends. Of course, by now feelings beyond "something to hold onto".
He has a controlling father who Ianto says broke his leg. Or there's the way he dies just as he's getting his life and relationships in order.
Toshiko Sato spends most of her time pining for a man who makes no secret of the fact he's having sex with dozens of other women 24/7 yet doesn't even look twice at her. Falls in love with a woman who turns out to be a heart-eating baddy. Finally gets the man she loves to agree to go out with her and he winds up dying. He then comes back as a zombie, replete with heaping loads of angst. And finally she has to comfort him as he's about to die WHILE dying herself. Oh yes, and she also gets brainwashed into falling in love with someone, so technically she's been raped as well. Seriously, if there's a female character in the history of the Whoniverse who's had it tougher I can't think of them.
Owen: Give me one good reason why I shouldn't keep screaming!!
We also have the whole reason she joined Torchwood in the first place. Her mother is kidnapped and she's forced to steal top secret info in order to free her. Then of course the kidnappers refuse to let Mum go to force her to steal more. Then she's arrested and thrown into a UNIT prison for who knows how long with no trial. Jack eventually comes to her rescue but only if she'll work for him. She'll be allowed to send an occasional post card to her mother....
Granted, she was actually only bound to Torchwood for a five-year term, after which Jack was willing to let her go, but then consider that she dies not too long before her contract with Jack expires. Even a 2010 edition of "Torchwood Magazine" states that Toshiko was the member of Torchwood least compatible with the work she did ("Greeks Bearing Gifts" can attest further to that), and yet she still held onto her duty and her friends (notice that of all the team, she's the one most frequently displaying Undying Loyalty to Jack). That poor, poor woman...
And then there's Owen, whose first encounter with Jack involved his fiancée dying through alien parasite, being repeatedly told that it didn't happen and that it was him going crazy, got his heart broken by a time-displaced pilot, got savaged by a Weevil deliberately after being abandoned by said pilot, got shot in the shoulder for trying to bring her (and the two members of the team stuck in the 1940s) back, was forced to euthanise a giant space whale, was mindraped into a more nerdy persona (even if he didn't remember it), got killed by a doctor that he actually respected, came back as an asexual zombie just because his boss wanted the codes for the morgue (well, and because "I didn't want to give up on you", but still...), got possessed by The Grim Reaper and had to fight it off in order to stop it from completely coming through into our world (which, okay, was also a Crowning Moment Of Awesome) and is finally trapped in a nuclear reactor, still completely conscious as his body slowly decomposes.
There are also hints in "Adam" that his childhood wasn't exactly ideal; the memories of his mother he mentions when Jack is trying to get rid of Adam hint at abuse, or at the very least an extremely dysfunctional childhood.
Upon remembering her kicking him out of the house, at around 14 years of age? "That's the nicest thing you've ever done for me, Mum." God...
Jack himself is quite woobie-ish. At the age of about fifteen or so, his father dies and his brother is taken in an attack on his home planet. His mother blames him for the loss of his brother. He fights in a war and him and a friend get captured by the enemy, and his friend is tortured then killed in front of him. After that Jack joins the Time Agency, where they wipe two years of his memories. He then meets up with the Doctor, gets shot by Daleks, resurrected, left on an empty space station and has to time-jump to the mid-1800s, where he discovers he can never die. Then he is blackmailed into working for Torchwood but has to take over when the whole team is killed by one of their own. After creating a new team, he is pretty much betrayed by all of them over time, then killed when they stage a coup to open the rift. After saving the world, he leaves with the Doctor, who he loves and has been waiting for for over 150 years, only to discover that he was left on the space station on purpose, the Doctor can't stand to look at him and he is stuck being immortal. He then spends a year in captivity being tortured by the Master. When he comes back to Torchwood, his brother (who he had been searching for since the beginning) comes back evil. The brother buries Jack alive, so he spends 2000 years dying and coming back, and kills two members of Jack's team.
Then there's Children of Earth wherein he gets blown up, comes back to life in agony as his skin and tissues grow back, watches Ianto die in his arms, and then has to kill his own grandchild to save millions and in the process gets (even more) estranged from his only daughter.
According to John Barrowman himself, to Jack, Owen and Toshiko were his students, almost like adopted children - he was "guiding them", so to speak, something which upon examination can be seen in his relationships with them (while Gwen and Ianto are more like partners to him, to Owen and Tosh he was frequently The Mentor). Ponder that, and then consider how much it must have hurt to lose them the way he did (through his own failings).
Speaking of Children of Earth, Anti-Villain John Frobisher, most especially in his final scene.
Gwen is falling into this trope, too. She tried desperately to save her father only to lose him during Torchwood: Miracle Day.
Sarah Jane herself. Her best friend, her parents and her fiancé all have to die as a result of the Trickster's interference (made worse because the Trickster brought them back as a part of his nefarious plans, forcing her to lose them all over again). Then there's The Lost Boy, when she's so distraught by Luke being taken away (and her near incarceration) that she nearly shuts herself off from her team.
Clyde Langer, as seen in "The Mark of the Berserker". His dad (a loving but often rather selfish man) walked out on the family when Clyde was ten (with his wife's sister), and moved to Spain. Because of this, he tries to act tough to the point that he hides some of his talents (such as skill at cooking and talent at art) from his friends out of insecurity. When said Disappeared Dad returns (having run away because his girlfriend is pregnant), he's forced to confront these issues... which results in temporary Mind Rape and emotional manipulation before he's finally able to reconcile with his dad and realise that his friends are still there for him... It's for all these reasons that this troper considers "The Mark of the Berserker" to be one of the most powerfully emotional SJA stories ever made (after the "Trickster" stories, of course).
The Skullion slaves from The Man Who Wasn't There. Made to operate a simulation of a dead man (lest they be tortured, maybe lethally if Harrison got really mad at them) so that their tormentor to make us want Frick and Frack's computer.