Let It Ride. Jay Trotter (played by Richard Dreyfuss) is practically the Trope Codifier. As the movie tagline states: "He drinks. He smokes. He gambles. He curses. He thinks about committing adultery. You'll love him." His best friend Loomey is even more of one.
Darth Vader in Star Wars is responsible for many of the Empire's atrocities, particularly killing the Jedi. He did so in an attempt to save his wife from dying, but this ends up happening anyway as a result of his own actions. And (he thinks) his unborn child(ren) died with her. And before that, there was his mother. Then there's the fact that the whole galaxy hates him for trying to do the right thing. Palpatine convinced him that the Jedi were trying to overthrow the Republic and sends him visions of his wife dying, so Anakin tries to save her by learning the secrets of the Sith, only to be overcome by the Dark Side. Then his wife dies, his best friend dismembers him and leaves him to burn to death, and he has killed the rest of his friends. The only person he has left is his worst enemy, Palpatine - who got him into this mess to begin with - until he learns that his son, Luke Skywalker, is alive. Jerkass Woobie indeed.
Joe Dick in Hard Core Logo. He can be amazingly self-centered, he's an unrepentant liar, and he gets his closest friends caught up in his self-sabotaging antics, but he obviously cares so much in his own screwed-up way that you wind up feeling sorry for him. Especially considering that he shoots himself.
Wikus van de Merwe in District 9 is a (fantastical) racistObstructive Bureaucrat who enjoys working for a corporation that evicts aliens from their homes. However, in the course of the film, he gets contaminated by harmful fluid, is nearly vivisected, becomes a fugitive from his employers and criminals, is separated from his wife, who believes that he cheated on her with a prawn (as the aliens are called), and eventually turns into a prawn whose only form of contact with his wife is via sending her "flowers" made out of scrap, just as he did as a human. In addition to this, he redeems himself over the course of the film, helping the aliens and even risking his life for them.
Harry Osborn from the Spider-Man movie franchise. Also, his father, Norman Osborn. Also, Peter's pretty much always been The Woobie, but in the third movie, he becomes a bit of a Jerkass after gaining the Venom symbiote.
Luke from Cherrybomb. While he undeniably behaves like a Jerk on several occasions, he does have a huge Freudian Excuse - he suffers appalling abuse and neglect at the hands of his family - and is clearly very emotionally vulnerable. The fact that he's tall, dark, and Bishōnen (i.e. the fact that he's played by Robert Sheehan) probably doesn't hurt either.
Inception: Mal. Yes, she ruined Cobb's life by framing him for her suicide, but this was only because she had spent so much time in the dream world that she was unable to distinguish what was a dream and what was reality. This led to her killing herself, convinced that she would wake up in reality. In the end, all she wanted was to go someplace where she could be happy forever.
Buffalo '66: played to the hilt with Billy. He's a total jerk, braggard, liar, and kidnapper, but only because he's led such a humiliating and pathetic life, in part due to his absentee parents.
Mark from The Social Network. He's an Insufferable Genius who discards people when they're no longer useful to him, but one of his lawyers finds out that much of his behavior is a Jerkass Façade, and he's actually significantly more lonely and vulnerable than he lets on.
Louis Winthorpe in Trading Places. He was a snobby blue blood commodities broker who ends up being framed for embezzlement and drug dealing, gets incarcerated, loses his home and wealth, and gets shunned by all his friends and fiance, who's also led to think that he's been cheating on her. The shock of all this proves so much that he gets driven to suicidetwice. He gets better after he learns that he went through all that because of a bet by his bosses of only one dollar, and he gets back at them magnificently.
The titular character of Hedwig and the Angry Inch is this in spades. He/She gets a botched sex change operation in order to obtain a Citizenship Marriage out of East Germany and, upon arriving in America, has to work as a prostitute to survive. She is also a snappy, bad-tempered diva who treats her band members like absolute shit - esspecially Yitzhak - which delves into outright psychological abuse at time.
Wolfgang Amadeus Mozart in the 1984 film Amadeus, a Jerkass and Insufferable Genius, with an Annoying Laugh to boot. Once he gets around to writing the Requiem Mass, though, he starts breaking down physically and mentally, and you can't help but feel sorry him.
At first, Bender from The Breakfast Club comes off like a punk with no reason behind his behavior, but it's later revealed that he has a very bad home life stemming from his father's abuse. He doesn't really change by the end of the movie, but your impression of him is softened considerably.
Several characters from the Pirates of the Caribbean series — but mostly Davy Jones and Norrington.
Raymond Shaw from The Manchurian Candidate. Yes, he's a cold, misanthropic jerk, but judging from what's implied about his childhood, it'd be amazing if he weren't. And that's not even counting what he goes through over the course of the film. The universe just hates this guy.
Henry VIII as portrayed in Anne Of The Thousand Days. He'll do anything for a male heir, no matter how unethical, unlawful, or unpopular, but all he gets for many years are daughters and stillborn sons. Small wonder that after the fourth failure, he shouts, "I am accursed!" His ex-wife, as badly as he treated her, pities him.
Sidney Falco in Sweet Smell of Success, largely because most people he meets seem to loathe him before he even gives them reason to (which, granted, he probably will). And because his boss, JJ Hunsecker, is just so much worse.
From The Final: barring Dane, all of the other outcasts(Andy, Ravi, Emily and Jack). They've been warped by years of abuse at school and unhappy home lives. Even as they torture their abusers, they want to keep the one guy who was nice to them away from it all.
Hugo: The Station Inspector. His leg was crippled in World War I, and beneath his stern, relentless persona is a lonely man who is harsh on orphans because it reminds him of the pain of being one himself.
The Marvel Cinematic Universe version of Loki is very much this trope, both in Thor and in The Avengers. On the Jerkass side, he kills an awful lot of people, to the point that even Thor seems to consider him to be this trope. However, you can't help but feel sorry for him when it's revealed that he's actually an adopted Frost Giant and it's revealed that his main motivation is to prove to his (adoptive) father that he is a worthy son. This also overlaps with Woobie, Destroyer of Worlds.
Nicholas Garrigan in The Last King of Scotland is a conceited, ignorant and selfish individual, constantly chasing the skirts of married women. However, seeing him getting meathooks shoved through his chest and then suspended from the ceiling, does make one feel sorry for him.
