Ghostbusters: The eponymous busters have to Cross The Streams to do it, but they defeat Gozer the Gozarian, an ancient god worshipped by the Hittites, Mesopotamians, and the Sumerians around 6000BC that would take on a Destructor Form from the thoughts of humans in the area and wreak havoc once it was summoned into our world.
We came, we saw, we kicked its ass!
Conan the Destroyer: What to do when you involuntarily helped the return of an ancient monstrous god? Wrestle him and rip off his horn with your bare hands, of course!
In Dogma, when Silent Bob kills the demon Azrael with Cardinal Glick's driver. Granted, the clubs in question were blessed by a priest (because the priest would be the kind of guy to do that), but when mortals are taking out demons you can't be picky about the methodology..
Subverted in Sin City where this very act is invoked (sarcastically) as a metaphor for doing something that is completely impossible.
Hartigan: And after I pull off that miracle, maybe I'll go punch out God.
Loki taunts every hero he speaks to and at minimum holds his own in direct combat. During the final battle he comes face-to-face with the Incredible Hulk. He's barely gotten 3 sentences out before Hulk grabs him and starts with the Metronomic Man Mashing, knocking him silly and taking him out of the fight. "Puny God."
There's also the matter with the hordes of aliens, their flying fighters, and space whales that invade Manhattan. The team manages to make several great god-killing punches (starting with the Hulk's One-Hit KO and ending with Tony Stark's Nuke 'em at the end the game.
Hellboy features its titular demonic hero being swallowed by the tentacled God of Chaos. Fortunately Hellboy was wearing a belt of grenades which he then detonated, blowing the creature up from the inside, leaving Hellboy remarkably unharmed.
Stacker Pentecost: I've never believed in the End Times. We are mankind. Our footprints are on the moon. When the last trumpet sounds and the Beast rises from the pit — we will kill it.
In End of Days (1999): Arnie solves the problem of universal evil by simply shooting the Devil with a bigger gun than previously attempted.
In the "Dark Dungeons: The Movie!", Debbie ends up summoning Cthulhu by playing too much D&D and in the end she defeats him through the power of prayer.
The Syfy Channel Original MovieBa'al: The Storm God plays with this trope. While the military succeeds in severeing Ba'al from his power source with a nuke, the actual one to punch him out is another god, El, who the heroes summon to defeat him. Humanity still weakened Ba'al and gave El the opening, however.
In Man of Steel, the military manages to knock Faora unconscious with a missile.
Understandable, given that Clark had just damaged her Cool Helmet, causing her to begin experiencing the same sensory overload that had crippled Zod moments before. A missile exploding in her face would no doubt be overwhelming, super-powered or not.