Roy took a level too. In the beginning, he was basically just a snarky team leader. The only time he showed his inner awesome was rescuing Elan from a situation he wouldn't have been in if he hadn't abandoned him in the first place (and him taking down Xykon, but that was via deus ex machina). After his little trip to heaven, he suddenly becomes more serious, has a worldly air around him, beats on a half-dragon-half-ogre, most of a bar in a barfight, gets ranked top of the list after beating Belkar (whose awesome used to be far above him) and even bopped Haley's uncle across the room. Aside from asking Belkar to find him a cartographer ("...this is a cart of gophers, isn't it?"), after being resurrected Roy has not made one bad descision or done anything that has come back to bite him.
"Beating" Belkar? More like one-shotting him with a plank of wood.
Belkar, but more like regained his level of badass. He comes down with a curse caused by his mark of justice. Then when the curse is broken, this happens. Complete with a kiss at the end!
Redcloak took a literal level in badass in this strip and the two following, showing off his newfound powers by soloing the entire Resistance and leveling its base.
In a more plot important example, Dave, the nerdy, chain-smoking everyman grows more and more badass over the course of the series, finally ending in his becoming the most powerful Mad Scientist in the series, curb-stomping Helen, Mell, and Madblood with ease and coming pretty close to destroying the world.
Torg of Sluggy Freelance took his level in badass during the That Which Redeems arc. Being stuck in an alternate universe with demons hunting you all the time will do that. Afterwards he seems to have settled back into a Crouching Moron, Hidden Badass.
Torg had been gradually — very gradually — ramping up in badassery from the start of the comic, where he was portrayed as geeky but normal, unlike explosion-happy Riff. It's only when he's placed in a world where everyone else is a total wimp (throwing pies is considered a heinous act of violence, and their version of a "nuke" is a leafletting campaign) that he finally emerges as a true Bad Ass.
It's easy to forget that, yes, he still owns a sword that can kill demons and gods if he allows it to feast on the blood of the innocent. Until somebody gives him a reason to pick it up again.
It's also worth keeping in mind that, prior to That Which Redeems, he succeeded in killing off Aylee's Evil Clone, who had just defeated Bun-Bun. Bun-Bun prefers to pretend that the whole thing didn't happen, and nobody feels like arguing the point.
From the time Torg got the sword in the Stormbreaker Saga, his badassery was more or less incidental/accidental. It wasn't until after That Which Redeems that it became remarkable. He appears to have taken another level during Aylee-Code Boom, becoming a casual zombie-slayer.
Demons are obviously tougher than the different "zombies", so it doesn't really suggest a further level-up.
Agatha takes several levels of badass in Girl Genius as she evolves from from the hopeless klutz of Polygnostic University to a Spark at or above the level of any previous Heterodyne.
Gil's evolution from a bored pupil constantly tested by his father for basic worth into a man capable of facing down his father, and an army of war clanks, is a clear example. See here for evidence.
More recently, Boris, the Baron's personal secretary, has suddenly shown his ability to not only take down a Jaegermonster, but actually beat him until he gives up classified information. This is actually a classic example, in that there was no on-screen intermediate development.
Tarvek either Took a Level in Badass or been playing Crouching Moron, Hidden Badass, surprising even his cousin-cum-bodyguard Violetta with his competance. Likewise, it appears Wooster, Gil's "valet", was doing much the same thing, as was Zola. Never mind The Unstoppable Higgs. Pretty much all the major and secondary characters in Girl Genius started as Badass, Took a Level in Badass, or aren't very important characters...yet.
Mentioned again. This is either a single continuity nod to the fans who insisted it was real, or will become the most epic 3rd line ever.
The character Cale'Anon from the webcomic Looking for Group. He starts the series off rather clueless and useless, and in the first comic gets blasted to cinders by Richard. By the third or fourth issue, he's changed a little and very soon is pulling stunts like this and this .
For some of the more unconventional crossovers in the Hellsing fancomic And Shine Heaven Now, the characters from that crossover have done this. The prime example is Madeline from the books of the same name: a sweet schoolgirl in the books, a regenerating vampire hunter in Shine.
Rumy from Fans!!, like everyone else, had already come a long way from the Ordinary High School Student with martial arts training by the end of the fifth book, but after the five-year Time Skip she comes off as a battle-hardened Lady of War.
Jack Noir does this too when he kills the Glorious Monarch after he gets fed up with the ridiculous costumes that he's forced to wear and then takes her ring for himself
The Parcel Mistress starts out as just a simple mailwoman who wouldn't hurt a fly. By the end of Act 5 she's a space-warping One-Man Army on a Roaring Rampage of Revenge, and one of the most powerful characters in the comic.
And then there's Jade, who was a competent, if underpowered latecomer to the game, and her Alternate SelfJadesprite — a depressed, completely ineffectual fussbudget. By the [o] intermission, Jade is easily holding her own against the Big Bad, partially because the spirit of her dead dog and surrogate parent won't let him fight her, and Jadesprite is in control of her emotions enough to deliver a tactically-critical piece of hardware to another character. In [S] Cascade, Jade and Jadesprite ended up merging into a combination of a God TierWitch of Space, a First Guardian, and a Sprite — making her the most powerful heroic character and second only to Lord English in absolute power.
Criminy of Sin Fest has grown a massive pair in about a week's time. Went from meek nerd to telling the resident JerkassHolier Than ThouKnight Templar Seymore off, digging his way into the maw of hell for Fuschia, then holding his own in a fight with a demonic pitch fork. Awesome.
Dubious Company handled this very subtly. At first, they have trouble fighting anything other than Kreedor's rookies. Later, the pirates attack Mary and Sue, AKA: The Sues in their sleep and still need to fight dirty and outnumber them. Then during the rematch at Kreedor's castle, the pirates are barely holding their own going one-on-one. Later still, The Sues, Stus, and Tiren team up against a dragon. The pirates' Tiren holds out the longest.
