Nothing says "This is dramatic, ominous and/or heavy foreshadowing!" like an ionic ground-to-air charge-release — in other words, lightning, and the accompanying thunder. Whether underlining the villain's apparent success, or the heroes' last-second arrival, you can just bet that the thunder is anything but a random result of the global weather-system.
There are variants of this:
The Thunderous Underline marks a recently-spoken sentence or word as particularly important, illuminates a recently-arrived character as particularly dangerous and/or sinister, or provide appropriate mood lightning for a villainous laugh. This is frequently lampshaded, subverted, or just plain mocked, though it still gets played straight on occasion.
In The Thunderous Confrontation, a fierce thunderstorm provides an appropriately chaotic background to a battle — of weapons or of wills. Usually, it will be the final, climactic confrontation between hero and villain, and you can just bet that the weather will clear up as soon as the hero's won. Frequently, the thunderstorm will play an active part in the battle, with lightning striking exposed targets, starting fires, causing trees to fall, or just making the Airborne Cavalry unable to come to the hero's aid. Almost always played straight.
A Storm Is Coming adds thunder as a sound effect to a dramatically brewing storm as part of the Foreshadowing. Often far off in the distance and with its lightning not visible; conversely, if lightning flashes had not had audible thunder earlier, thunder may indicate that the storm is closing in. It may also thunder with the storm clouds directly overhead but no rain yet.
Used to underline Aiden's threat before he reveals he's kidding.
Used to underline traded threars when Herzog and Standish have their chat at the duck pond.
Anime and Manga
In episode 20 of Noir, after the two titular assassins have just finished a running battle across the rooftops of Paris against a small army of suit-wearing killers with creepy masks, Chloe makes her appearance, standing on top of a chimney — with a flash of lightning behind her. Which is a good tipoff that something important is about to happen, considering that Chloe usually favors the Stealth Hi/Bye.
In the second episode of the Ranma ½ anime, Tatewaki Kuno introduces himself as "The Blue Thunder of Furinkan High" with an appropriately-timed ominous thunder. This is a deliberate subversion, as Kuno is ye originale Martial Arts Butt Monkey for the entire series.
A later episode (and manga chapter) shows Ryouga showing up at the Tendo Dojo for the first time, having tracked down Ranma there. Just as he declares his intention to kill Ranma, lightning illuminates his features (a bit more dramatic in the animated version, where it lights up the whole scene.)
In Yu-Gi-Oh! GX episode 88, a single bolt of lightning, from a single cloud that came out of nowhere in a clear blue sky, punctuates Jun Manjoume "Thunder" (it's a pun on his insistence toward the use of honorifics after his name) calling out his catch phrase, signifying his return to some semblance of normalcy.
In Fist of the North Star, several of the major villains are first introduced amongst flashes of lightning, but none get a more thunderous introduction than Toki Actually Amiba, whose first non-flashback appearance is surrounded by repeated bolts of lightning. Nevermind that he's INDOORS. It's somewhat appropriate for his Strapped to an Operating TableMad Pressure-Point Expert persona.
Gundam SEED Destiny plays this straight during Shinn and Athrun's battle between the Destiny and GOUF, in which Rey's lines are often met with lightning strikes, as well as Athrun's "You're being manipulated" line to Shinn.
Used in Popotan when Mea defeats Keith in episode 10. Almost, that is.
In the third episode of X1999, blurring the line with Thunderous Confrontation. Lightning flashes repeatedly as Kamui confronts Fuma at an abandoned basketball-court and they both have a premonition about their future battles - and at the same time, across town at the Tokagushi Shrine, Nataku attacks Kyuogo to steal the Divine Sword, again amidst the flashing lightning. It hardly counted as a confrontation, however, considering how outmatched Kyuogo was. By the time something approaching a fair fight develops - between Nataku and Kamui - the thunder has already passed...
In A Garfield Halloween, Garfield and Odie encounter a creepy abandoned house out in the woods. When a bolt of lighting flashes behind it, with the obligatory peal of thunder, Garfield lampshades it by commenting, "Nice touch!"
Films — Animated
Kung Fu Panda uses this form of the trope to punctuate Tai Lung's escape: as he stands on the precipice outside the exploded doors, he sends Zeng flying back to the temple to "tell them the real Dragon Warrior is coming home."
And later when he arrives at said temple, appearing in the time it took Shifu to blink.
Spoofed in Wallace & Gromit: The Curse of the Were-Rabbit. Lord Victor Quartermaine has come to ask Reverend Hedges how to kill the were-rabbit. Loud thunder accentuates every dramatic sentence until Victor gets annoyed and closes the shutters so they can talk normally.
Bollywood loves to play this one straight. At the beginning of Kabhi Kushi Kabhie Gham , two characters argue about telling X that his brother was adopted. Cue reveal that X is in the room and heard everything. CUE LIGHTNING.
Early in The President's Analyst, a patient of the eponymous psychiatrist reveals he's a government agent concluding a background check on him. He suggests taking the conversation outside as the office could be bugged. The doctor scoffs at the thought, until the agent casually points out the bug he'd planted. As the doctor ponders what he's been unaware of, thunder rumbles in the background.
In the movie Night of the Demon, Dr. Holden is skeptical about a deadly curse that's been placed on him. As he compares notes with the niece of his associate who had died after a similar curse, he realizes he may have been passed an essential slip of parchment. As he rushes for his briefcase to look for it, thunder booms. That can't be good...
Used to the point of parody in the 'Ten Little Grifters Job' episode of Leverage. Dramatic events and statements are often underlined by a thundercrack, and the lighting flickering on and off due to the house running off of its own, fairly old, generator.
All the time in Mortal Kombat. For example, when Raiden explains to Liu Kang that Shang Tsung has stolen the souls of thousands of opponents. Raiden is the God of Thunder with a penchant for theatrics, so he's probably doing it on purpose.
The film version of Godspell: "And from that moment, he began to look out for an opportunity *booooom* to betray him."
In the 1999 film version of With Fire and Sword lighting and thunder occurs when Bohdan Khmelnytsky introduces himself. Khmelnytsky is Anti-Villain at worst, but the trope is played completely straight.
The thunder continues to sound at suitably dramatic moments; when they start squabbling, when Humbert finds Charlotte reading his diary in which he's confided his lust for her daughter, and when Humbert realises she's been killed in a car accident.
In Doc Savage: The Man of Bronze, lightning flashes and thunder sounds as Doc announces that his father was murdered.
In Discworld, the country of Uberwald provides this as a basic service to the Mad Scientist and Vampire Lord types that inhabit it. At least one vampire, newly arrived in Ankh Morpork, is slightly discouraged when, upon making dramatic declarations, thunder fails to oblige. Later in the novel, when it finally comes around, he indulges, repeating, "Big...scary...castle!" as the thunder rolls.
Also in Guards! Guards!!, Vimes is looking at the aftermath of the "battle" with the dragon, says "Do you know what? I think it went somewhere". When the thunder rolls on cue, he mutters "All right all right, it wasn't that dramatic."
The Two Towers novel, Book 4 Section VIII "The Stairs of Cirith Ungol". As Frodo and Sam pass by Minas Morgul, lightning and thunder crash inside Mordor and Minas Morgul answers in kind. It's a prelude to the departure of the Witch-king's army.
Septimus Heap: The battle between The Vengeance and the Dragon Boat occurs during a thunderstorm that was engineered by DomDaniel.
In A Wolf In The Soul, Jack Crowe makes a dramatic statement and is very disappointed when this doesn't happen. He tries a few more times. Still doesn't happen.
In the Star Trek classic episode "Spectre of the Gun": as the Earps and Doc Holliday walk to the O.K. Corral for the final gunfight, lightning flashes overhead and thunder rolls. Partial overlap with Thunderous Confrontation.
Played straight in the Star Trek: Voyager episode "Muse". B'Elanna Torres has crash-landed on a primitive planet and is being helped by Kelis the poet, who takes her for a powerful mythical being called an Eternal. B'Elanna wants Kelis to get dilithium from a local warlord's hunting grounds, which he is understandably reluctant to do. At that moment a coincidental roll of thunder sounds. Kelis' eyes widen as he says, "Did you..." B'Elanna plays it beautifully, leaning forward menacingly and saying "Don't get caught."
Until recently, Count von Count from Sesame Street had Dramatic Thunder accompanying the final result as he finished his counts... a few years ago, it was discontinued since it might scare children, however, and now only appears on special occasions.
In A Muppet Family Christmas he counts "two worried frogs" looking out the window as Miss Piggy is lost in a blizzard. Kermit and Robin react as if the thunder is just more of the bad weather they're looking at.
Parodied in Ugly Betty, when Big Bad Wilhelmina meet Betty on the roof dramatically, while her assistant Marc created thunder sounds with a sheet of metal around the corner.
Lampshaded/parodied in Friends. Phoebe's part time navy boyfriend has just returned on shore leave and she is hoping for some fun, but she has just contracted chicken pox. When he meets her she has covered her face with a shawl and won't show it to him. He convinces her to and she reveals her chicken pox scarred face to him with a lightning flash in the background. He jumps in fright and she gets upset. He responds by saying "No no no, you look fine it's just, the lightning, it was a very unfortunate coincidence."
NCIS. A roll of thunder is heard right after Ziva and Abby's slapfest in "Hiatus", much to McGee's alarm. However Ziva does not kill Abby.
In the episode "Ham Radio" of Frasier, Noel shakes a sheet of metal to create the thunder for Frasier's play.
Also played straight in "Surprise" when Angel loses his soul; he wakes up in pain to the accompaniment of a crash of thunder, and has time to stumble out into the rain before turning into the evil Angelus.
In the Drake & Josh episode "The Bet" the boys are told to bring an umbrella to Megan, who is at a friend's house. They don't and she comes in the front door soaking wet with thunder announcing her entrance.
Happens twice in "Number One Fan". The first is Lampshaded when Josh tells the kids he is upset they won't brave a gentle rain shower to go camping. Cue the thunder. Josh, showing a slight fear, then continues. The second happens a few minutes later when Drake comes in angry at one of Megan's friends with thunder crashing as soon as he enters.
A musical example in the Disturbed song "Haunted", used at the beginning of the song along with a bell.
The webcomic A Miracle of Science has the Mad Scientist Dr. Haas living on a partially-terraformed Venus, where it rains almost all the time — providing plentiful Dramatic Thunder for his Mwa-Ha-Ha's and declarations of "I'll show them ALL!". Even if he's indoors without any windows around.
In Metal Gear Solid 3: Snake Eater, The Sorrow is established to have limited weather-control abilities. In the webcomic The Last Days of Foxhound, he's occasionally seen applying this ability to provide appropriate emphasis for either his own words or a dramatic confrontation — which does, incidentally, border on Thunderous Confrontation territory.
Liquid: Was that necessary?
The Sorrow: No, but very appropriate.
The Boss. "He's after..." *thunder* "THE PHILOSOPHER'S LEGACY". The Sorrow might've even provided it for her just so she'd look cooler...
Lampshaded in GPF, in thesetwo strips. At that point, the characters are already getting tired of it.
Abel's Story, a side-story for the webcomic DMFA, invokes this rather sadly in this strip. It's difficult to calm down someone whose mother you nearly killed when a mage provides dramatic lightning to underscore your statements.
Sluggy Freelance has also used this a few times, either with actual thunder, or merely a footnote saying *Insert Dramatic Thunder Here*.
In Everyday Heroes, superhero Mr. Mighty introduces himself to the neighbors with dramatic lighting and thunder. Lampshaded in this episode, where you can see the pull-chain Mr. Mighty uses to trigger the lighting flash. Also has Professor Odious and his Scary Shiny Glasses.
Played straight in the What's New, Scooby-Doo? episode "The Vampire Strikes Back"; first the Castle Thunder sound is used at the beginning of the episode (but is presented in very low-fidelity quality and sticks out like a sore thumb), but then newer, more realistic (and LOUDER) thunderclap sounds are used for the rest of the episode (driving the show more toward realism compared to the classic "campy" cartoon feel the original series had). The newest (and more darker and realistic) show, Scooby-Doo! Mystery Incorporated, featured this as well in a couple of episodes, including a Thunderous Confrontation in an episode featuring a dangerous battle on an old building's roof.
Used on Jimmy Two-Shoes to highlight Heloise's Evil Laugh. Then it turns out the lightning was Jimmy flipping the lightswitch quickly.
Subverted in the episode "Bridle Gossip". After Applejack says "The Everfree Forest!", there's a clap of thunder, which turns out to actually be the clattering of pots and pans, knocked over by Spike while sneaking a snack.
Played straight in "The Best Night Ever", to accompany Fluttershy's Evil Laugh.
Used a number of times by Princess Luna in "Luna Eclipsed". Rainbow Dash also spends a good deal of time pranking ponies by invoking the trope.
A frequent occurrence once the ponies enter the ancient castle in "Castle Mane-ia".
Accompanies Gogmagog's mooks in Korgoth of Barbaria when they open the door to the tavern where Korgoth is currently residing.
Lampshaded in Phineas and Ferb with the Regurgitator who apparently uses a device for this. Prior to the reveal, Doofenshmirtz questions the thunder and lightning several times.
Fairly Oddparents: Lampshaded, among other things, by Timmy's friends, Chester and Aj, when their ball lands in the yard of Dr. Bender's home, a reviled and hated dentist who loves to mock the dental hygiene of other children and gave his attack dogs braces so they could have perfect teeth. Said home is revealed to be a Victorian style house surrounded by a fence with razer coil barb wire amongst completely dark scenery (it's daytime out) complete with giant moon.
Chester: Dude. Didn't you see the lightning and hear the weird music?
Episode 25 of Death Note, where L finally winds up on the pointy end of Light's Evil Plan and dies, takes place during a nasty thunderstorm. (Also qualifies as a Thunderous Underline - recall the line spoken right before the lightning strikes...)
Shortly before the final showdown between Cloud and Sephiroth in Final Fantasy VII: Advent Children, the latter nonchalantly raises his hand to summon dark storm clouds that cover the entire battlefield. These seem to serve no other purpose than to emphasize the apparent epicness of the whole affair, which is further evidenced by the fact that a conspicuously well-timed bolt of lightning appears just as the two lunge towards each other.
Street Fighter II: The Animated Movie opens with Ryu and Sagat's fateful duel in a windswept grassland, thunder flashing across the skies. The two combatants' Ki Attacks, which involve arcs of electricity as far as the movie is concerned, match the environment nicely.
Oda Nobunaga in Sengoku Basara's anime comes complete with a red-glowing ominous thunderstorm that follows him around wherever he goes. Needless to say, it's impossible to not have a Thunderous Confrontation with Nobunaga.
In Gundam SEED, Kira's and Athrun's epic duel halfway through the series takes place in a thunderstorm.
Gundam SEED Destiny has Shinn and Athrun face off in a thunderstorm, complete with dramatic strike at the exact moment Shinn impales Athrun's GOUF with his BFS.
In one of the chapters of Don Rosa's classic The Life and Times of Scrooge McDuck, Scrooge fights a duel with swords against the scion of the Whiskervilles — ancestral enemies of the McDuck clan, while a thunderstorm rolls across the Scottish Highlands. The thunderstorm, as it turns out, plays a key role in the end of the duel...
Turnabout Storm uses this in the introduction of the murder in Part 1. There's an interesting twist in that the lighting isn't there just for the dramatic effect, but it's also the cause of death.
Films — Animated
The Disney version of The Jungle Book has Mowgli's confrontation with Shere Kahn take place just as a thunderstorm rolls in.
The final battle of The Lion King pits Simba against Scar during a thunderstorm. The brushfires that are ignited by the lightning plays its part in the battle, as per usual...
Kim Possible's movie, "So the Drama," features an epic thunderstorm during the final battle, beginning with thunder as the villain's plan goes into action and culminating in a fistfight atop the roof in the pouring rain.
For a Disney production, the storm is built up to in a surprisingly subtle way — Kim's hair begins gently blowing in the wind in a previous scene, and later clouds slowly roll into view through a background window.
Played quite straight in Kung Fu Panda: as the villagers evacuate the Valley of Peace and Shifu waits outside the Jade Palace for Tai Lung, ominous storm clouds are gathering. By the time their inevitable fight has intensified and the snow leopard kicks Shifu out through the roof, dramatic lightning bolts are streaking across the sky. What makes this interesting, though, is how it plays with the trope: instead of the Thunderous Confrontation being between the hero and the villain, it's between the villain and the Old Master. And while the weather does clear up to become beautifully sunny, this coincides not with the hero's victory, but his arrival at the battle scene to save his master. In all likelihood this is meant to imply Po's wisdom in interpreting the Dragon Scroll, granting him the knowledge and power to win, somehow mystically dispelled the storm—particularly since with the passing of the darkness, the snow leopard's attacks somehow seem weaker and more foolish, and Po has a much easier time of it than Shifu did. Rather Anvilicious, but quite effective nevertheless.
Films — Live-Action
In The Crow, the final fight against Top Dollar takes place on a church roof during a thunderstorm. The storm ends as The Crow stands victorious...
At the end of the first The Neverending Story film, as the Childlike Empress is calling out to Bastian from within the apocalyptic ending of the book, a violent thunderstorm is occuring in the real world.
Inverted in Back to the Future. Thunder foreshadows the approaching dramatic storm — but this is a Good Thing, a critical plot point, to get Marty back home. It's played straight right at the end of Back to the Future II.
In The Go-Between, the ambient temperature rises higher and higher as the passion grows between Marian and Ted, and then when they finally manage to consummate that passion there's a terrific thunderstorm. At this point Marian's mother catches them in the act and mayhem ensues.
Janine and Candayce's confrontation in Dinoverse starts after Janine's struck by lightning and continues as the storm rolls over them, though when it's faded to a light rain they're not quite through yet.
In the Outer Limits TOS episode "Specimen: Unknown", a thunderstorm rages overhead as deadly alien plants spread out from a spaceship crash. The humans are in despair as they believe that the rain from the storm will cause the plants to spread more quickly. Instead the plants shrivel and die when exposed to water, so the storm actually saves the human race. This is a rare case where the thunderstorm works to the good guys' advantage.
President Bartlett: What the hell...? If this isn't a metaphor for powerlessness, I don't know what is.
The Wild Wild West episode "Night of the Bleak Island", while the heroes are trying to deal with a deadly hound and a murderer.
Tabletop RPG example: The Dungeons & Dragons module I10, The House on Gryphon Hill, ends with a climactic chase of the Big Bad Creature through a violent thunderstorm. But it takes place in Ravenloft, where such things are to be expected...
In Shadow of the Colossus, the battle with the Final Colossus is accompanied by a heavy thunderstorm. Concidentally, the Gray Rain of Depression starts right after Agro seemingly dies. After the battle is over, we see the main hero lying unconscious at the feet of the destroyed colossus while the sun shines brightly in clear sky.
Even Bully couldn't escape this — the Final Confrontation, up and down the sides of the school's belltower, is accompanied by a well-timed thunderstorm. And flocks of black crows, just for good measure
The dramatic Ninetails battle in Ōkami, fought atop the great mansion of Oni Island. Since you've learned to control lightning at this point, and the foe enjoys flourishing her highly-conductive sword, this works to your advantage.
One of the phases of the Final Battle repeats this, with lightning flashing as the boss raises its sword-shaped arms.
The first Wily stage in Mega Man 9 has thunder on the screens before the mini-boss area. It's not exactly the most exciting battle around (specially since it's a reappearing boss), but it works as a warmth welcome to the final area in the game.
Rhythm Heaven Fever: During the last stretch of Samurai Slice, where the music reaches its climax, lightning strikes with each successful slice. Yes, lightning strikes perfectly in sync with the battle and music.
The Order of the Stick battles Miko Miyazaki during a thunderstorm. Naturally, the always Genre Savvy Elan realizes that things are about to go south as soon as the first peal of thunder resounds...
Used here in Bleedman's Powerpuff Girls Doujinshi. Even Cartoon Networks characters can look pretty dramatic with some appropriately-timed lightning thrown in.
Outright invoked through the power of Steam Punk science by the titular Girl Genius during the Battle of Mechanicsburg. A modified electrical superweapon is used to 'charge' the atmosphere, even while an (apparently completely coincidental) rainstorm rolls in to deliver a thematically-appropriate downpour. Finally, the lightning is climactically released to revive the sleeping Genius Loci of Heterodyne Castle...
The Homestuck song Rex Duodecim Angelus is set during the climactic battle between the trolls and the Black King, and contains multiple thunder special effects in between character Leitmotifs. Presumably an effect of the Rule of Cool, because the only weather known to be present during that fight was a meteor shower.
In the Avatar: The Last Airbender episode called "The Southern Raiders", Katara's confrontation of her mother's murderer is punctuated by a storm that's a bit less than a major thunderstorm, but shows off just how powerful a waterbender she is.
One confrontation between Robin and Slade in the Teen Titans cartoon has a dramatic lightning strike - interesting in that they are fighting in Slade's underground base.