In the movie The African Queen, the titular ship actually succeeds in destroying the German warship "Louisa" (actually Königin Luise) even after capsizing herself in a storm, as the "Louisa" happens to run into the overturned African Queen, striking the detonators of Charlie Alnutt's home-made "torpedos". In C. S. Forester's novel the Queen anticlimactically sinks in a storm and the "Louisa" is finally sunk by two modern British gunboats transported piece by piece overland and then assembled on the west coast of the East African lake. (In the film the captain of the "Louisa" also receives a villain upgrade, condemning Charlie and Rosie to be hanged. In the novel he decides it would be uncivilised to have the two executed as spies so he hands them over to the British under a flag of truce).
Tim Burton's film adaptation of Alice in Wonderland gives the Mad Hatter this treatment; he goes from a silly joke character (as most of the cast in the original work) to a silly joke character who charges into battle with a Scottish claymore. Arguably all of the characters in the movie, as well, to some degree.
Harry Potter films took this both ways with Buckbeak. On one hand, they gave Buckbeak his own Crowning Moment of Awesome by showing him protect Harry and Hermione from the werewolf, which wasn't in the book. On the other hand, the sixth and seventh books described him flying around attacking Death Eaters, which wasn't in the movies. A borderline example, if you will.
Bilbo Baggins apparently Took a Level in Badass between the original novel "The Hobbit" and the 2012 movie. While the story is basically the same, Bilbo is in general a lot more quick-witted and competent in the movie, and on several occasions—most notably the encounter with the Trolls—manages to accomplish more in moments where he was saved by someone else in the book.
In the book in fact, he doesn't really start pulling his weight until he saves the Company from the spiders. Which may mean he becomes badass faster in the movie than in the book.
In fact, the entire company is more badass than they were in the book.
Iron Man 3 does this to Aldrich Killian. In the comic book storyline Extremis, Killian commits suicide at the start of the comic after being spurned by Tony. In the movie, Killian initially looks like he will follow his comic counterpart, but does not go through with it and becomes the main villain of the movie. He is revealed to be the real Mandarin, orchestrating terrorist attacks using the Extremis formula and posing a very large threat throughout the movie.
Supporting villain Tal Hajus was a lazy Villainous Glutton who rarely moved from his throne (and got curbstomped in less than a paragraph when he did move). In the film he's in much better shape, much more active, and apparently younger, though he still gets curbstomped. Being a Big Bad Wannabe in an action/adventure story apparently doesn't let you catch a break.
In The Wonderful Wizard of Oz, Glinda is a relatively tame character that does help the heroes, though through indirect means, which translated into the 1939 film adaptation. In Oz: The Great and Powerful, Glinda is a much more active character seeking to avenge the death of her father, the previous wizard who uses her magic to battle the Wicked Witch of the West and play a large part in getting the people of Oz to revolt against the Wicked Witch.
Also applies to the Wicked Witch of the West herself. In the book and the 1939 film, she does have spells that can help her accomplish her goals, (including poppies and an enchanted hourglass that ends a person's life when the sand runs through it); but both are foiled (by Glinda's snow and The Scarecrow, Tin Man, and Cowardly Lion rescuing Dorothy) and she ultimately meets her end by being splashed with water. Now, she has fire-based magic and actively tries to harm the people of Oz in part for being manipulated into becoming the Wicked Witch of the West.
Daphne in Scooby-Doo was transformed this way. She even beats someone up in the live action film.
Holmes and Watson's portrayal in the 2009 Sherlock Holmes, although not nearly to the degree that some viewers accused it. Watson was a veteran Army doctor in the books, while Holmes was a martial artist and bare knuckle boxer with surprising strength. The movie turns them both into outright action heroes who take on multiple opponents at once in hand-to-hand combat and defeat all manner of armed attackers.
Skyfall does this to Miss Eve Moneypenny and to lesser extent, Ralph Fiennes' Gareth Mallory, new M after the death of Judy Dench's M.
The sequel gives this treatment to Khan. Not that Khan wasn't always a badass, but in addition to Prime Khan's charisma and intelligence, this version of Khan is shown to be much more physically powerful, going straight into One-Man Army levels.
In the Superman comics, General Zod was one of Krytpon's top military advisors, but often relied more on his planning skills than doing actual fighting. The character's film portrayals have helped make him a much bigger threat. Superman II portrayed Zod as a charismatic leader that took full advantage of the fact that the gained powers from Earth's yellow sun; as displayed in the film's fight scenes. It proved to be so successful that it was integrated into the comics and became a key factor in every subsequent adaptation that featured Zod. In Man of Steel, Zod is even genetically bred and trained for war; and proves to be more than a match for Superman.
From the third film, Sentinel Prime, who mostly appeared in comic series to serve as Optimus Prime's predecessor who gets killed by Megatron, and in as a Jerkass in Transformers Animated who got beat up every appearance he made. Here, he's Optimus Prime's mentor and never made out to be helpless and after being revealed as the film's Big Bad, actually defeats Optimus in both their fights.
In The Transformers, Mirage was a good fighter, but often tried to avoid doing so by relying on his invisibility powers. In Transformers: Dark of the Moon, Mirage, now named Dino, is a badass Ferrari with a thick Italian accent and knives coming from chains on his arms and is much more active in combat; ripping apart one of the Dreads during the car chase on the DC Parkway and playing a large part in the final battle in Chicago that takes up the bulk of the film's third act.
V for Vendetta features a tricky one for Gordon Dietrich. The movie turns him into a chubby, middle-aged comedian (played by Stephen Fry, no less) when he was a younger, more physically imposing career criminal in the book. Then again, the film also has him defying the Party's laws by hiding banned books and films in his house, and openly mocking Chancellor Sutler on his show (which he is eventually executed for), which is far more badass than anything the character did in the book.
Much like the Peggy Carter example from Captain America, Mariko Yashida is a much more capable and physical badass in The Wolverine.
Longtime X-Men villain Toad was originally conceived as a deformed, sniveling hunchback who served as The Igor to Magneto. His super power was he could hop... really high because of having very low-grade super-strength, concentrated in his legs. However, after the first movie, in which stuntman Ray Park played him as a wisecracking martial artist with wall-crawling abilities and a tongue that he could use as a whip, the comic book character was re-imagined and upgraded to have the same powers, thus making him more capable of holding his own in a fight with other heroes. Also, he could spit slime projectiles.