During the Joan of Arc Campaign, the first part of the mission in which you attack Paris involves you going to meet up with the King's reinforcements. When you reach your destination, two poor-quality units come out and greet you with this line, which indicates that the King has betrayed Joan.
Militia: We are all the king could afford to send.
News Announcer: ...and the international community had just announced its recognition of the election of the new president Gemaal Sheik Charrief ... and now, sources report that he and all his government were assassinated in what appears to be an unclaimed attack.
It's time to end this little masquerade. There ain't no Atlas, kid. Never was. Fella in my line of work takes on a variety of aliases. Hell, once I was even a Chinaman for six months. But, you've been a sport, so I guess I owe you a little honesty. The name's Frank Fontaine.
During the Chapter 5 trial, Nanami starts acting strangely, ending with this:
Nanami: "But...there’s nothing they could have done...since even if they had wanted to confess...they couldn’t have...Because they weren't made that way. So...I want you guys to try and guess. (...) The Future Foundation spy, the traitor hidden amongst us...who do you think it is?"
Rozalin: ...No, you don't understand. The reason I cannot tell you is...I-I don't know where my father is! I have never even met him before!!
In Dissidia 012, you unlock the Confession of The Creator scenario (Scenario 000) after completing Treachery of the Gods (Scenario 012) and Light to All (Scenario 013). Those latter two are numbered after the "cycle" of war in which it takes place. As per the story of the original game, the heroes break the cycle and go home after the 13th cycle. In Confessions of the Creator, which doesn't seem to take place anywhere in the ordinary story, the Mured Moogle (Cid of the Lufaine) tells you his story as you make your final approach to Chaos. In it, he casually mentions that in the 13th cycle, everyone on Cosmos's side, including the goddess herself, died and were purified. You may write this off as perhaps a misnumbering. Maybe there was a 0th cycle or something. And then he talks about an 18th cycle.
DoDonPachi: Complete the game normally, and the Commander commends your efforts and tells you it's time to take a well-deserved rest. Fulfill the conditions for the 2nd loop, however, and...
"That was a good fight. You should be commended...Psych! You're dead meat!! Enemies you've been fighting against, supposedly 'Mechanized Aliens', were actually. our (sic) guys, the missing battlefleet you learned about in the academy. You were killing our guys without knowing it!But I planned that all along! And your death...would be a nice finishing touch to my whole scheme. My special forces are the best of the best and they will be welcoming you with fierce fier (sic) power. See You in Hell!"
In DoDonPachi DaiFukkatsu, Colonel Longhena has two versions of the "welcome to 2nd loop" speech, depending on which version of the 2nd loop you unlock. Either way, he declares his intent to "build a new order"...
Dragon Age II, at the end of the quest "Alone": "You said you never wanted those markings, but that's not true! You wanted them; competed for them!"
In Merrill's quest "A New Path", she notices that the Pride Demon who taught her Blood Magic is not present at Pride's End, and suggests that something must have happened to it. Keeper Marethari, now possessed by the demon, arrives and says "I happened."
In The Elder Scrolls V: Skyrim, at the end of the quest where you have to negotiate a truce between the Stormcloaks and Imperials, Delphine walks up to you (if you haven't talked to her yet) and says this:
Delphine: "Oh, and one more thing. We know about Paarthurnax."
Etrian Odyssey. All this time you thought you were in a medieval world of sorts. Then comes the fifth Stratum, named Lost Shinjuku. And yes, it's referring to Shinjuku, Japan.
Fahrenheit: "A Mayan sacrifice. That's what it was."
Fate/stay night has several. Due to the nature of the narration, some hit the reader more than the characters, and vice-versa.
Archer: Trace, On.note For those not familiar with Fate/Stay Night, this little phrase is the one Shirou always uses to summon swords, revealing that Archer can also do this — because he is Shirou from the future.
FEAR: Paxton Fettel's words "You and I were born from the same mother."
Technically, it's not spoken, but toward the very end of the game, the camera pans down to show the name on the Origin project folder: Alma Wade. That one word changes the context of about 90% of the entire game.
After the credits, the very last words in the game. "There is some good news, however. The first prototype was a complete success." Spoken by Genevieve Aristide, the president of Armacham.
In the endgame of Final Fantasy I, the Warriors of Light journey to the world of 2000 years in the past, to confront the demon Chaos. They descend deep into the then-pristine Chaos Shrine...and encounter a disturbingly familiar face:
Garland: Do you remember me? I was once known as a knight of Cornelia.
Final Fantasy IV looks like it sets one up when Cecil and company travel to the moon and meet FuSoYa, when he reveals that his brother, KluYa, was Cecil's father. But that's just to set up the real Wham Line - Golbez: "My father? His name was...KluYa".
Also earlier on, when Kain approaches Cecil in Fabul. The wording varies based on the translation, but the effect is the same.
"Twelve years ago, I lost one of my most prized Genomes. I created him and sent him to Gaia to disrupt the cycle of souls there. You are that Genome."
"I constructed the Genomes to be vessels for the souls of Terra when they awaken. But 24 years ago, I gave life to a Genome that was very much like you. His will was too strong to make him into a proper vessel, and I even considered discarding him. But then I thought that I should put his strength to use. I sent that Genome as my servant, to disrupt the cycle of souls on Gaia. The one I sent to Gaia might also be called your brother...and his name is Kuja."
Balthier: He made airships...weapons... He even made me a judge.
Ashe: You were a judge?
Balthier: Part of a past I'd rather forget. It didn't last long. I ran. I left the judges, and him... Cidolfus Demen Bunansa, Draklor Laboratories' very own Doctor Cid. That's when he lost his heart to nethicite, lost himself. And I suppose that's when I lost my father.
Also these, provided you didn't read the instruction manual, which lists all the characters:
Judge Ghis: This is hardly the courtesy due the late Ashelia B'nargin Dalmasca.
Primarch Galenth Dysley: Why don't you leave, Jihl? Or rather...take your leave? Humans have no place here.
Primarch Galenth Dysley: I am fal'Cie. My name is Barthandelus, voice of the Sanctum, and Lord-Sovereign of the Cocoon fal'Cie.
Earlier we get two in one:
Oerba Yun Fang: I'm from Gran Pulse. The world below you all hate so much. My partner and I had turned to crystal there and gone to sleep. The reason Cocoon's in such an uproar is the same reason you're here now. Vanille and I woke up.
Half-Life is relatively straightforward with a team of scientists accidentally opening a rift to another dimension that leads to an alien invasion of Earth. Except for the mysterious man with the suitcase who shows up all over the game, sometimes unlocking doors for Gordon Freeman and sometimes blocking his way, until revealing at the end that everything turned out just as his "employers" intended, and then puts him into suspended animation until he needs him again. In Half-Life 2 he sets Gordon Freeman loose and manipulates things in the background again, hinting that there had been several parties that were interested in securing his services. The real whammer comes near the end of Episode Two when he implants a message into the mind of the daughter of the scientist who led the experiment that resulted in the alien invasion.
G-Man: "When you see your...father...relay these words: Prepare for unforeseen consequences."
Which gets an even bigger punch as you have to be a huge fan of the first game that was released 12 years earlier since "Unforeseen Consequences" is the name of the level immediately after the experiment goes wrong and aliens invade through the dimensional rift.
Shortly before that while speaking into Gordon Freeman's mind, he is shown sitting on the computer of the security guard who first mentioned that on the day of the experiment the computer system of the facility was going crazy, but "seemed back to normal", revealing that he wasn't just opportunistic in using the dimensional rift for the goals of his employers, but actually created it on purpose.
Immediately after the above line is delivered, the aforementioned scientist tells Gordon that he was told to "prepare for unforeseen consequences" right before the experiment began.
Eli: You know who I'm talking about. Our mutual friend.
This is the first time someone has acknowledged the existence of the G-Man. Eli also tells Gordon that the G-Man brought the crystal used in the experiment to Black Mesa in the first place, confirming the earlier hints that he was responsible for the disaster.
343 Guilty Spark: Failsafe protocol: In the event of unexpected shutdown, the entire system will move to standby status. All platforms are now ready for remote activation. Commander Keyes: Remote activation? ...Where would someone go to activate the other rings? 343 Guilty Spark: Why, The Ark, of course. Arbiter: And where, Oracle, is that?
Arbiter: When the Prophets learn of this, they'll take your head! Tarturus: When they learn? Fool, they ordered me to do it.
Librarian: The Didact is here. The Didact is gone...It is said the Master Builder executed you on the San'Shyuum quarantine planet. You are now all I have. You are now all we have.
The Captive: We meet again, young one. I am the last of those who gave you breath and shape and form, millions of years ago. I am the last of those your kind rose up against and ruthlessly destroyed. I am the last Precursor. And our answer is at hand.
Primordium had one near the end as well:
Guilty Spark: Some say [the Librarian] is dead, that she died on Earth. But this is demonstrably untrue...And after a hundred thousand years of exploration and study...I know where to find her.
The Beast: Humanity is dead. Help me save what I can.
Jade Empire: "Your abilities have grown immensely. But it also does my heart good to see that you have remembered the basics of what I taught. Eventheflaws."
Early on in the game, after the attack on Two Rivers by the Lotus Assassins, Sagacious Zu will say "I...I was one" immediately after talking about them (the context varies based on your dialogue choice).
Metal Head leader: Don't you recognize him? The boy is you, Jak.
Katawa Shoujo has a few, often accompanied by the music stopping.
In Emi's route
Hisao's Narration: "Emi's there, yes. But she's in a wheelchair"
Hisao finds a bottle in the shed, and the label tells him why Emi brought him there.
"Personal lubricant - lemon flavored."
In Hanako's route, this exchange between Hisao and Lilly not only takes the scene into a completely different direction (especially in that it forces Hisao to re-evaluate how he sees Hanako), but takes it into a completely direction than the equivalent scene in Lilly's route.
Lilly: There is another person, though, that has been a subject of worry for me as of late.
Lilly: That person is you, Hisao.
In Lilly's route.
Akira: When our folks told me that when we were at their place, though, they also gave Lilly a summons to rejoin them in Inverness.
Xigbar/Braig: "Oh, thank you, Sora's Heart, for leading him right into our clutches. Aren't hearts great? Steer us wrong every time." Sora: "You know, don't you? Because you all have hearts!" Xigbar/Braig: "It's about time you noticed."
A second one comes almost immediately after this one, also involving Organization XIII:
Malak: Even the combined power of the Jedi Council couldn't completely destroy your former identity, could it?
Kreia: Know that there was once a Darth Traya. And that she cast aside that role, was exiled, and found a new purpose. But there must always be a Darth Traya, one that holds the knowledge of betrayal. Who has been betrayed in their heart, and will betray in turn.
Joel: Why the hell are we smuggling an infected girl?
After Ellie and David fight off a group of infected:
David:: A few weeks back I ah...sent a group of men out to a nearby town to look for food. Only a few came back. They said that the others have been slaughtered by a crazy man. And get this, he was a crazy man traveling with a little girl.
and a bit later, once Ellie finds out the truth about David's village.
David: I know you're hungry, you've been out for quite some time.
Blood Omen: He is the last! [Moebius points at Kain and swords are drawn.] Destroy him!
Soul Reaver: The blade is vanquished. So it unfolds...and we are a step closer to our destinies.
Soul Reaver 2: My god...the Hylden...we walked right into their trap. Raziel! Janos must stay dead!
Defiance: The Soul Reaver, pure of all corruption...this is what it is for. This is what I am for. The two become one...both Soul Reavers...together...and the Scion of Balance is healed...And I am not your enemy...not your destroyer...I am, as before, your right hand...your sword.
Magic Emperor Ghaleon: "Now...who shall be my queen?" (Dramatic close-up on Luna, still stuck in her Heroic BSOD)
Make It Good: Context dependent: He hands back the letter opener. "On this; no good, Inspector. The only fingerprints we got were yours - you must have handled it without gloves on. However, the blood is the deceased alright." when the player has used gloves while handling it.
Manhunt 2: "Everything's gonna be alright, honey."
Mass Effect 1: There is a realm of existence so far beyond your own you cannot even imagine it. I am beyond your comprehension. I am Sovereign.
The very next line also acts as one:
Shepard: "Sovereign isn't just some Reaper ship Saren found. It's an actual Reaper!"
As well as every single word that Sovereign says, which forever altered any ideas anyone had about the story of the games, cementing Sovereign's status as a Walking Spoiler:
Sovereign: "The cycle cannot be broken. The pattern has repeated itself more times than you can fathom. Organic civilizations rise, evolve, and at the apex of their glory, they are extinguished. The Protheans were not the first. They did not create the Citadel. They did not forge the mass relays. They merely found them. The legacy of my kind."
Dr. Weil: "Hehehehehe! Excellent, Zero! Your power is extraordinary, for a fake."
Perhaps not quite as shocking, but there's this exchange from the first MMZ, leading right into the final segment of the game:
Cyber-Elf X: "I'VE CRACKED THE SECURITY SYSTEM OF THE TRANS SERVER...I'M SORRY THAT IT TOOK SO LONG...BUT NOW YOU CAN ENTER NEO ARCADIA WHENEVER YOU WANT." Zero: "You...You're the one who gave the Z-Saber to me..." Cyber-Elf X: "NOW GO. TERMINATE THAT COPY OF ME...TERMINATE WITH EXTREME PREJUDICE..."
Mega Man Juno: Have we met before? Oh, please forgive me. You are a purifier model, assigned to the direct command of Mother. As I recall, you were designated Mega Man Trigger. Please forgive me, I did not recognize you in your current configuration.
And then from the sequel, we have this:
Mega Man Volnutt: The keys!
Yuna: Now this is a problem. She plans on executing the Carbon Reinitialization Program!
Mega Man Volnutt: Carbon Reinitialization Program?
Metroid Fusion: "Samus, this is your last mission. Go to the Operations Room and adjust the station's orbit path to intercept SR388. Then return to your ship and escape. Move quickly, and stay alive. That's an order! Any objections, Lady?"
The SA-X generally causes a lot of these:
"I have learned the identity of our mystery saboteur...Samus, it's an X mimicking you. ...The SA-X is mimicking you at full power." "You know that the X reproduce by asexual division. Because of this mechanism, there are now no fewer than 10 SA-X aboard the station."
Even before that, Wheatley's laugh turning into an Evil Laugh lets you know that things have officially gone south.
"PART 5! BOOBY TRAP THE STALEMATE BUTTON!" Yes, this came right after the trap was activated, but you'll probably be too shocked to realize what happened when the line is said.
The Perpetual Testing Initiative we have one given after the "Computer!Cave" "arc" that completely turns the notion of "Cave Prime" on its head:
Cave Prime: Whoa! Chariots chariots. For some reason, some of the audio was bleeding through in this universe. Don't know if you were catching the subtext there, but that computer Cave is crazy. So: Greg was right. As of now, we are cancelling the genetic lifeform disk operating system initiative.
From Portal, notable is that this was not in the original game and was patched in as part of an Alternate Reality Game add-on more than two years after release.
Robot: Thank you for assuming the party escort submission position!
Professor Layton and the Curious Village, Professor Layton to Inspector Chelmey: No inspector, it has quite a bit to do with you. If there is any criminal element involved in this case...then it is you sir! The finger-pointing that goes along with it has since been repeated in every game.
Professor Layton and the Unwound Future, Celeste reveals herself as a temporarily time-shifted Claire by saying "You've taken good awfully good care of that hat I gave you", and also, in the line before, addressing Layton by his first name rather than "Professor".
Cross: You should pick your friends more carefully, Mercer.
Alex: I'm not human. The revelation...it freed me. It killed me. I'm not human. *uneasy chuckle* Alex is just the role I play. Part of me was relieved...and part of me died. Just another disguise, right? So ingrained...so real...even I believe it.
And also from Director McMullen
"Alex Mercer died. He died threatening to release the most deadly virus in history on the people of New York."
"Earth and Secilia have vanished. Likewise, those that developed the "RAY" technology and all evidence of its existence have been wiped away. No record of R-GRAY craft was found, and no R-GRAY craft has ever returned."
In The Reconstruction, everything looks like it'll be fine and the world will be saved, but this banks on the fact that the third Watcher hasn't messed anything up. But that's okay, you're still on schedule and know where he is...or do you?
"Third Watcher? You mean Donz? I thought he went down with you guys, Ma!"
Jean Bison: I ain't like you boy, I ain't stew-pid. When y'all were unconscious me and my boys paid a visit to your hideout and found all them Clockwerk Parts. Lucky thing, too; Arpeggio was willing to plunk down a King's ransom for the whole lot. I even threw in the Talons.
"I want to go home! I want to go back to my house by the hill! I want to see my mother!" The girl was shouting now, her face wet with tears. "But I know she's not there! I knew all along that she wasn't out there in the sky! Because...because..."
Jade: That's what I would say if I was an emperor, with a country and people to look after. As your friend...I feel compelled to stop you.[...] I'm sorry.
Sometime before that, as the party is discussing Asch's mad plan to die in order to remove the miasma from the world, and the party is trying to think of an alternative, they ask Jade, who knows the situation better than anyone:
Jade: ...The only alternative I can think of is even crueler.
There's also always this reveal, if you haven't figured it out already due to the massive amounts of Foreshadowing:
Asch: That's right. You're a mere replica. A second-rate copy of me!
Tales of Vesperia: Although what's said isn't quite so important as the voice that says it.
Raven/Captain Schwann: I suppose there's no fooling the nose of a dog.
"Victoria, are you ready to give Mr. Garrett his compensation?"
Thief II: The Metal Age: In "Life of the Party", one of your objectives in the Mechanist Tower is to investigate a series of prerecorded messages that Karras has left behind for his guests in order to see if you can find out anything useful about his work. In addition to the ones scattered about the tower, there is one final prerecorded message you can find in his office, which is empty, locked up and closely guarded— you play it, and what's the first thing you hear?
In Alliance of the Golden Witch this is even used with what the character can't say when Battler tries to say that he is the son of Asumu (his mother) and can't, effectively proving that Asumu ISN'T his mother, causing alot of dropped jaws
999's sequel, Virtue's Last Reward, has some as well: for example, Quark casually drops this bombshell in Tenmyouji's route. As a bonus, it's not a wham unless you've played certain other routes or the first game...but if you have, it makes things about ten times more complicated.
Quark: (referring to a photo of young Akane from 999): "Oh, she was the old man's 'first love'."
Earlier in Operation 006, Vorkken leaves a message, and Immorta translates it.
Immorta: It's in Rhulloian. [...] The language of the comet Rhullo. The world that Vorkken... and I... call home.
And after the boss fight with Vorkken.
Immorta: A space pirate? Really?! The people of Rhullo loved you! And now you're a miscreant! A malefactor! Another grub in the garbage pile! That, and you don't seem to know when you're beat, my dear brother!
Joshua's got to have the best, though. "It was me, Neku. I'm Shibuya's Composer." And let's not forget Kitaniji's "Your points have been tallied, and the Player to be reborn decided. Congratulations...Shiki Misaki." and, slightly later on, "This time, you’re playing for...Shiki Misaki.".
The Another Day Secret Report, obtained by reading all of the previous ones, and defeating the Bonus Boss. By reading the others, you'd discovered the existence of a Fallen Angel who had aided Minamimoto, and learned that the writer of the Reports was Hanekoma, who is an Angel who is looking to find and stop the Fallen Angel. However, when you read the Another Day report, he says that there's a reason he doesn't want to meet up with the alternate version of himself: "You see, I am the Fallen Angel who taught Minamimoto how to refine Taboo Noise. Minamimoto owes his successful rebirth to the corrections I made to his flawed Taboo refinery sigil. I must hide in Pork City for fear that my alternate self in this world may report me on sight."
The dragons' flame sealed my fate. The world of the living can no longer comfort me. Place the crown upon my head, Tirion. Forevermore - I will be the jailor of the damned.
Define reappears. He's visible in one of the portals you can go into while fighting Yogg, his voice is heard early in Icecrown Citadel, and his body is chained above the Frozen Throne all throughout your fight with the Lich King. All in all, that one had plenty of foreshadowing.
Also, at the Wrathgate itself:
Grand Apothecary Putress: Death to the Scourge and death to the living!
Loken has one final line to add insult to injury after capturing Thorim
As for your life, mortal. I will be generous. After all...why would I destroy my most useful servant? I waited for you for weeks inside that Hyldnir minenote He is referring to the questgiver that set you on the entire chain in the first place, thereby leading you to bring Thorim to him.
Toward the end of the Creepy Crate quest for Hallow's Eve, on the Alliance side (a similar series of events occurs for the Horde version) you have the option of turning it over to Anson Hastings, or to Hudson Barnes for safekeeping. If you choose Barnes, he will tell you this.
I know this will seem like betrayal, but Mr. Hastings has made an offer I simply cannot refuse. My apologies, (player).
Toward the end of Hour of Twilight, the Twilight Prophet reveals himself.
Archbishop Benedictus: And now, Shaman, you will give the Dragon Soul to ME.
One comes up in Cataclysm's ending
Alexstraza: But now we must see it...with mortal eyes.
In "Dagger in the Dark", this exchange takes the mission into an unexpected turn when Rak'gor tries to kill Vol'jin.
Vol'jin: Da Saurok, 'dey not born - 'dey was created. Flesh shaped an' bent. Dis be the blackest of magics, mon!
Rak'gor Bloodrazor: Yes! The power to shape flesh, to build warriors. This is what the Warchief wants!
Vol'jin': Garrosh playing god? Making monsters? Dis ain't what da Horde is about!
Rak'gor Bloodrazor': He knew you were a traitor! (stabs Vol'jin).
In "Path of the Last Emperor, after you reach the top, the questgiver talks about himself.
Seer Hao Pham Roo: I was going to teach you a lesson, but instead, it is you who have taught me. You see, when I was young...(voice gradually changes) when I was young...when I was young...I was EMPEROR.
Xenoblade has two within five minutes of each other.
Egil: ( talking to someone we know to be called Zanza) "I also desire that, Arglas"
Dickson: (after shooting Shulk) You shouldn't have done that, little brat.