Let's list cutscenes variations

Mother Base cutscenes apart, Metal Gear Solid V has one of the most unique and interesting thing I've ever seen in a video game: the cutscenes in the game adapts to the way the player plays and to Game Overs, and it's really little but amazing details. Even now, one year after the game was originally launched, new things are still being discovered, and even more may be waiting to be discovered aswell.

Tell me any scene that is missing that you might know and I'll add it to the list.

METAL GEAR SOLID V: GROUND ZEROES

MISSION [Ground Zeroes] Rescuing the prisioners in the cells before rescuing Chico will change the cutscene, as the prisioners won't call for help, a part of the cutscene is ommited and there won't be anyone near there. And more (Thanks u/Can-Of-Dicks for this one!): If all the guards are cleared then when Chico is being rescued instead of alerting the other prisoners by shouting, a jeep approaches and a Marine can be heard exiting it near the tents. Snake then chokes Chico out to make him be quiet. Rescuing Paz first and putting her in the ground will also trigger a cutscene and will change a bit Chico's cutscene. Putting Chico in the ground before putting him in the Helicopter will trigger a scene in which he gives you a cassete tape. If you don't do that, they won't talk and the cassete tape will drop from the Helicopter as it takes off, adding some more to this other little cutscene. Also, rollinf back and forth in the ground several times will trigger a secret cutscene with a XOF patch that was in Big Boss's Sneaking Suit. (Thanks u/CallMehEpic for remembering this one!)

MISSION [Intel Operative Rescue] S-Ranking the mission will change the line Hideo Kojima says during the cutscene after the mission is complete from "What took you so long?" to "Snake, that was perfect!".

MISSION [Déjà Vu/Jamais Vu] Tons of special easter eggs/scenes, including Kojima Productions logo, Canonical and not-canonical Metal Gear games logos, Flashbacks, "FoxDie virus" infecting the Fox Engine, Genome Soldiers, skins (Gray Fox, Solid Snake, White and Commando Armor for Raiden), Snatchers, etc. "You may erase the markings, but the memories will never disappear."

There is some extra conversation aswell, including alternate/extra debriefings if you extract Glaz and Palitz (The Eye and The Finger) instead of eliminating them during MISSION [Eliminate Renegade Threat] and by getting the true cassete tape after interrogating one more time the undercover agent after discovering the first location contained a false cassete tape. Several prisioners through missions will also talk, and guards during specific moments or through interrogation will give you unique conversations.

METAL GEAR SOLID V: THE PHANTOM PAIN

Characters appearance: Replaying some missions, for example MISSION 31 [Sahelanthropus] and not having Quiet anymore/never had her, will put a Diamond Dogs soldiers in her place during the "Return" cutscene. Plus, Huey and Child Soldiers might or might not appear during certain scenes, for example, the Nuclear Disarmament one (which Quiet, Huey, Child Soldiers and even Sahelanthropus can appear, or all of them can also be ommited depending on the story progress. This affects the birthday cutscene aswell with specific characters- for example if too early, Code Talker might also not appear)

Snake/Soldiers Gear: The gear you are wearing will be shown in the cutscene, even uniforms, for example Solid Snake or Raiden outfits, changing the cutscenes (some of them becoming really weird with them instead of Venom Snake). But the most impressive is soldier gear, the most notable one is if you have destroyed the soldiers helmet stock through Dispatch Missions before MISSION 30 [Skull Face], the XOF soldiers will appear without helmet, even in the landing cutscene of Skull Face and his bodyguards. That's some nice little detail.

While playing as a Diamond Dogs soldier, cutscenes without player interaction will fade to black and play with Venom Snake dressed in Olive Drab camouflage instead of the soldier. However, if you are playing as your avatar, the cutscene continues without switching to Venom Snake. (Thanks to u/shadotterdan for this one.)

PROLOGUE [Awakening] Sticking with Ishmael in the beds instead of hiding in the other side of the room fom the XOF soldiers in the Hospital will trigger a cutscene with both of them crawling together and hiding from the enemies.

MISSION 01 [Phantom Limbs] When rescuing Kazuhira Miller, you can actually have Venom Snake say "Kept you waiting, huh?" if you press the action button when he asks you to say the "magic words". If you do not rescue Kazuhira Miller in three in-game days (like Ocelot says, this is the time he have left), a special cutscene will play as Venom Snake find him already dead. (Game Over) You can also skip the Skulls cutscene and even not meet them if you change the the Helicopter landing zone pre-defined to any other, but only after playing the mission for the first time.

MISSION 04 [C2W] Destroying the Comms Equipment before doing the mission will skip it completely, not having the necessity of playing the mission. It's normally during this mission that you meet D-Dog. Specific cutscenes/appearance in cutscenes of him will only play if you fulton him during the mission. He will not appear during Huey's Trial for example, and Huey won't talk about him either (talking about he being a dog or a wolf). He won't be sitting near the Diamond Dogs Pilot in the Helicopter either during the return to Mother Base scene after capturing Quiet. His appearance in Mother Base as a puppy/his arrival and being ready for the deployment cutscenes are ommited too.

MISSION 06 [Where do the Bees Sleeep?] A special cutscene interacting with the mute Hamid prisioner (Silent Basilisk) will play if you get to him in the Mountain Relay Base before the soldiers transport them out from the post. In the other hand, if you let him be captured, if you follow him without trigger any alerts, a torture and execution of the prisioner by the soldiers will take place (E3 2013 animation from Camp Omega Prisioner Execution) and the Honey Bee will be in the hands of the soviets. If you don't take the weapon from them, another secret cutscene will play, as the weapon is taken away by Helicopter (Game Over)

MISSION 09 [Cloaked in Silence] Quiet specific cutscenes/missions/appearance in cutscenes only if you don't kill her. When Snake's is pointing the gun at her, not pressing any button will result in Snake sparing her. A lot of cutscenes in this one are ommited, for example the Jet Fighter pilot being shot, dancing in the rain (which is also optional, appears only if you have maximum bound with her), and her presence in cutscenes with other characters. There will not be a "Mission 45: A Quiet Exit" either. In the other hand, killing Quiet will trigger a little cutscene of her being reduced to nothing like a normal Skull.

MISSION 12 [Hellbound] You can choose if you will use or not the Prototype Walker Gear at Huey's Lab. Using it will trigger a cutscene of Huey activating the Walker Gear and Venom Snake taking control of it.

MISSION 13 [Pitch Dark] Child soldiers are being trained by an African Soldier in the first village. It's optional and you can see only through gameplay, during the day, and if you do not trigger any alerts. It's not a cutscene. This is what happened to the E3 2013 child soldiers training cutscene in the "Sins of the Father" trailer.

MISSION 16 [Traitor's Caravan] If you take too long to approach and fulton the the truck transporting the Yellow Cake, and he reachs it's objective, a cutscene will play as the truck is evacuated by boat. (Game Over)

MISSION 18 [Blood Runs Deep] The post-mission cutscene changes depending on the child soldiers you rescued, showing only the ones you took to Mother Base. It can show from one to all of them.

MISSION 19 [On the Trail] A helicopter taking the target away cutscene if he is alerted of an enemy, cancelling the reunion and getting away (Game Over)

MISSION 20 [Voices] If you stay at the "Devil House", the battle will continue with the Man on Fire normally, but if you try to run away, the path will be immediately blocked by rocks in an gameplay scene.

MISSION 21 [The War Economy] The target will cancel the reunion if you alert the Airport before his helicopter lands, triggering a cutscene of the helicopter flying away. (Game Over) Also you may find the guy's corpse along a project where it crashes if you take down the helicopter before it lands/go away.

MISSION 23 [The White Mamba] When Venom first meets Eli, he'll speak Kikongo during the cutscene if you have an interpreter. If you don't, he'll use English. There is also a Venom Snake vs Eli fight cutscene (from the E3 2014 "Nuclear" Trailer), it will only trigger if you defeat Eli inside his room. Plus, both of this cutscenes can be skipped if you shoot Eli from distance in the head with a tranquilizer shot. (Thanks to u/SwordOMighty for this!)

MISSION 28 [Code Talker] Gameplay effect. You can skip the Snipers Skulls battle, and if you do that, after you rescue Code Talker, they will be back and all the area will be covered by fog and the soldiers will be acting like puppets. Killing them in the first encounter will not trigger this.

MISSION 30 [Skull Face] If you don't follow Skull Face and stand still after the first encounter between them, he will say to you the quote "You don't want to listen what i've got to say, Big Boss?" (this one a friend of mine discovered some days ago, a little nice detail)

MISSION 31 [Sahelanthropus] In the Skull Face execution scene, if you do not press the button to shoot him, after some time Kazuhira Miller will take Venom's arm and point the gun at him shooting, adding some more to the cutscene. (Thanks for u/netokosovo for remembering this one!) But, if you choose to shoot him, pressing the button again and again will make Venom Snake shoot him three times triggering little flashbacks before the actual cutscene plays. (Thanks for u/ItalianJoe for remembering this.)

CHAPTER 2 [Race] Quiet's retrieving Shabani's Necklace in Mother Base. This one will play if you have Quiet, but is also tricky and some people say they did not saw it during their playthrough. That's because this scene will only play if during the time the cutscene is set to play, during Chapter 2, you have already constructed the second platform (2/4) of R&D section in Mother Base.

MISSION 35 [Cursed Legacy] Failing to extract the containers before the enemy Helicopter arrives will trigger a cutscene of the Helicopter coming to take the containers, then the screen will fade to black and you can hear a sound of the containers being extracted by the Helicopter.

MISSION 40 [(Extreme) Cloaked in Silence] Quiet will be using the Sniper Wolf outfit in this mission, through gameplay and cutscenes.

MISSION 46 [Truth: The Man Who Sold the World] The cutscenes during this mission will adapt with the face of your Avatar and the information you gave the game in the beggining of the Prologue. You can also see the face of your Avatar in the reflex of the Helicopter window inside the ACC.

MISSION 50 [(Extreme) Sahelanthropus] Sahelanthropus will have a different paint in this mission, resembling a skull, through gameplay and cutscenes.

There is also a lot of extra conversation and ALTERNATE DEBRIEFINGS depending on the outcome of the mission or the fate of the target.

MISSION 07 [Red Brass] Either extracting the Red Army brass or otherwise neutralizing them (ie, killing them) only after listening to their speech has Kazuhira Miller relaying to Snake the contents of their meeting.

MISSION 14 [Lingua Franca] Rescuing at least one British POW in addition to the Viscount will have Miller reveal to Venom Snake the Viscount's duplicitous nature and imply that he intends to have the Viscount undergo more severe interrogation for his earlier actions to his comrades before reporting on the delivering of Walker Gears to the various PFs, CFA included.

MISSION 19 [On The Trail] If the player either extracts the Major or otherwise neutralizes him after listening in on his conversation with his subordinate, Miller will relay to Venom Snake what the Major revealed on everything he knew about the events, including that ZRS was planning to kill an old man.

MISSION 21 [The War Economy] If the player decided to extract the CFA executive instead of killing him, Miller will debrief Venom Snake by revealing that the CFA executive wanted to join Diamond Dogs and reveal that it was his higher-up's idea to prolong the fighting with the implication that he didn't necessarily support it. Similarly, extracting the arms dealer will have Miller reveal that he was headhunted by SANR and that he wasn't actually its president, only receiving his orders from a cutout.

MISSION 22 [Retake the Platform] If the player extracts Mosquito, Miller will reveal Mosquito's past as a former Militaires Sans Frontières member. Mission 26: If the player extracts the Trafficker, Ocelot will relay what the trafficker told him about the Devil's House.

Also, there is even more prisioner and guards extra talk. (some of these are mission tasks)

And this not mention that there is a lot of special hidden scenes in Mother Base like the gone too long (Ocelot, D-Dog puppy, D-Dog low, medium and high bound versions), Quiet taking a shower, the ENTIRE Paz side story, GMP in red soldiers fighting each other, "you stink", happy birthday from staff and Quiet, Attack on MB warning (target known and unkown versions), NUCLEAR DISARMAMENT, etc.

Metal Gear Solid V is probably the most detailed game ever, even if it's "incomplete".

There is one special cutscene of Venom Snake walking through burned corpses from the E3 2014 "Nuclear" Trailer that might also be in the game. During the MISSION 13 [Pitch Dark], there is a village that looks the same with burned corpses, but there is no cutscene. The animation from the scene was maybe used for the MISSION 43 [Shinings Lights, Even in Death], but it remains unclear. Some also say that the scene was a part of MISSION 51 [Kingdoms of the Flies], which was presumably cut from the game. Or maybe the complete cutscene is inside the game, yet to be found? This Konami tweet hints that the scene might still be in the game: https://twitter.com/metalgear_en/status/648349984375508992 (Thanks u/SAURON120000 for the link!)

What are your thoughts?

I thank you all for the interest, it's an honor to contribute to NeverBeGameOver!

Like I said if any of you know any other scene that is missing from the list, just say. Thanks.

Sources: My experience with MGSV, friends, NBGO members, YouTube videos and Metal Gear Wiki.