All of the BAU team members became woobies at some point. Hotch, during the Reaper arc ("Omnivore" to "100"), is the best example of this show so far.
Some UnSubs are rather sympathetic , like Vincent Rowlings, Lucas Turner, Samantha Malcolm and so forth. Even ones like Adam Jackson/Amanda and Ian Doyle to some fans.
Spencer Reid. The guy was kidnapped and shot up with dilaudid to make him addicted, for Pete's sake. As Reid's actor himself described; "I've been kidnapped three times, held hostage twice, I've watched my best friend kill a man, I've seen a kid commit suicide in front of me, I've been shot and even set on fire," ...and that was only after the first 3 seasons. He's since been exposed to anthrax, shot (again), made it through a heroin addiction, been reunited with his absentee daddy after a decade, struggled with his schizophrenic mother, revealed his incredibly depressing high school experiences, been plagued by nightmares, not to mention threatened and generally targeted by Unsubs a couple more times And in Season 8, He finally seems to find a girl, only for her to be shot IN FRONT OF HIM in a murder-suicide by her stalker.
Aaron Hotchner. Gideon left, Haley left, he got blowed up pretty good and watched Kate Joyner bleed to death while they were stuck in front of Federal Plaza. And THEN he was stabbed nine times by The Evil Stabbity/Scrawny Bastard, Foyet, whose evil machinations require that Jack and Haley be put into protective custody, and Hotch not know where they are. He explicitly has PTSD now. He's bound to have the most EPIC of epic breakdowns. It's only a matter of when he breaks. Since that writing, he's lost his leadership position, he's got higher-ups doing everything they can to destroy his career, and Haley is now dead, leaving him a single father. What else are they going to do to this poor guy?
Jason Gideon. By the end of his character run, he's been made to feel personally responsible for the deaths of how many people? One of whom is his girlfriend, who's sliced up by a psychopath whose freedom he was forced to help negotiate himself. And that's just people we've seen or heard about in the series.
If it's possible for a single-episode character to be a Woobie, then Johnny McHale from "True Night" probably is one. His pregnant girlfriend, to whom he'd just proposed, was killed by a brutal gang who made him watch, then beat him and left him for dead. Then at the the end of the episode, he discovers that the experience caused him to have a psychotic break, and he's been running around killing people over the past few days without realizing what he was doing. He ends the episode locked sitting on the floor of an insane asylum, dialling his girlfriend's number over and over just so he can hear her voicemail, because that's all he has left of her.
All of the team members get their turn as woobie as lampshaded by the network in a "profilers in peril marathon".
Some of the would-be victims. Rebecca from "...A Thousand Words" is kidnapped by an unsub who commits suicide, leaving her in the hands of his pregnant wife. When the wife goes into labor, she throws the key Rebecca needs to escape out of her reach. Rebecca helps her give birth to a son, only for the wife to tell her to keep the baby away from her. Then she dies, leaving Rebecca with the newborn. As you might guess, by the time the team finds her, she's understandably freaking out. Or how about the father and daughter in "The Fight" who were abducted by the unsub, who forces the father to fight homeless men (in one case, to the death) or he'll kill them both? Made all the more heartwrenching by the fact that the father regrets not being the best father. Finally, the daughter agrees to leave with the unsub, if only so he'll stop forcing her father into any more fights.
The parents of the missing boy in "A Shade Of Gray". They're clearly loving parents who are distraught over their son's disappearance which makes it all the more difficult when The Reveal comes out that they (along with a cop friend of theirs) are covering up the fact that their son was not abducted, he was actually killed by his own brother, who doesn't feel a bit of remorse.
Despite committing one of the most disturbing crimes on season nine by far, Wallace Hines is this due to his heavy Mommy Issues.
Eddie Lee Wilcox is seen as this after his mother died from childbirth and his father committed suicide. Not only that, but after the traumatic childhood, he started to rob banks as an adult to support his family. Despite his certain outbursts, he really wanted to spend time with his daughter for one last time before commenting suicide himself due to his self-hatred.