Villainous example with Armstrong. After Raiden tells him "Maybe I was wrong about you", He picks Raiden back up, dusts him off, and gives him what can only be described as a handshake and a brohug at once, briefly showing that he not only has room to forgive, but genuinely wants Raiden on his side.
The few scenes that had Sunny made people's hearts melt.
More specifically, Sunny knows how much Raiden has suffered more than most. She believes that he's a hero despite everything that's happened, and Raiden in turn promises to go on protecting her and countless other children hurt by war.
Just the fact that her name is now "Sunny Emmerich."
The brief conversation about her adoptive father, Hal.
You can tell Raiden has a soft spot for Sunny, whenever he talks to her he does it with the same affable voice he used throughout Metal Gear Solid 2. Even when he's in the middle of the fight of his life he'll still make sure that she is not too upset by what is happening to him.
Bladewolf arriving in the boss battle with Senator Armstrong to aid Raiden. Bladewolf gives a speech about how he owes a debt to Raiden for saving him, and more importantly teaching him about the value of fighting for what you believe in. Bladewolf concludes his speech by saying it is his moral imperative to survive and preserve what he believes in, aiding Raiden being part of that goal, he then throws Raiden Sam's old sword which Raiden uses to defeat Armstrong.
Made even more awesome by the fact that Bladewolf claims that this course of action is his choice, in clear defiance of Desperado's intentions for him. As an AI he has claimed true sapience, being able to think and feel on his own merit. An astounding moment for any machine with intelligence.
Raiden also appears to treat Wolf as another person rather than a robot claiming he is taking revenge for him.
Bladewolf's interactions with Sam are fascinating. When Raiden inquires about Sam Bladewolf has nothing but positive things to say about the man. In fact Bladewolf shows slightly more affection towards Sam (at least outside of Codec moments) than he does to Raiden, shown at one point being petted and called "Wolfy" by Sam. Bladewolf even goes out of his way to discourage a battle between Raiden and Sam. You almost get the impression that Bladewolf is a dog that is trying to stay loyal to his old master (Sam) while still trying to serve the new one (Raiden) to the best of his ability.
Some of the codec conversations:
Raiden talking to Kevin about his and Rose's son, and how excited his son is to see him when he comes home.
Raiden talks about how much he admires Snake, and even implies that he may still be alive.
The encouragement your team gives you during the final battle.
During the Mexico level at one point Raiden gets ahead of Bladewolf, and Wolf apologizes for failing in his recon duty because falling behind has never happened to him before in a mission. He promises to Raiden that he will "redeem" himself and try better next time, only for Raiden to dismiss it as not being a big deal. Wolf presses the issue until Raiden concedes and accepts the (unneeded) apology. Seems like this dog wanted to impress his master on their first mission together.
After the final battle with Sam, Raiden's advice to Wolf about finding his own beliefs and ideals is one for two reasons. While he is not only encouraging Wolf be his own master, it is reminiscent of advice that Snake gave Raiden inside Arsenal Gear. Shows how Raiden is becoming Older and Wiser as well as being a Big Brother Mentor to Wolf in the same manner Snake was to him back in Sons of Liberty and Guns of the Patriots.
After Raiden unleashes his Jack the Ripper persona and enters World Marshal he will tell Courtney to leave the mission since he is just a plain murderer who enjoys his actions. Courtney completely opposes Raiden as she states that he is actually fighting to protect the infants kidnapped by the PMC and the Raiden she knows is not what he thinks.
What about Bladewolf finally getting a chance do to something other then fight at the end? After being shutdown after being declared a failure, and then reactivated, restraining-bolted and forced to fight, it's sweet to see him... just relax.
Made all the more comforting by the fact that Blade Wolf has a home with Sunny, where he will be loved and cared for like a member of the family. Not only does he get to talk to a fellow intellectual in the person of Sunny, but he can also be a canine companion to that sweet little girl instead of a killing machine.
During the ending of the Blade Wolf DLC, Wolf is talking to Sunny about his experiences prior to being rescued by Raiden. Sunny expresses her sympathy by saying how Wolf has been through a whole lot. Wolf doesn't deny that he's been through tough times, but then he begins to express his gratitude towards Raiden for freeing him. Wolf expresses that Raiden was just like him, forced to kill and forced to witness the darker side of humanity, but what inspired Wolf was how admirable it was that Raiden rose above his circumstances and fought for what he believed in. Sunny then expresses that this is why she believes in Raiden too, and begins to pet Wolf, which causes Wolf to wag his tail in elation. Raiden, you really do have some amazing people that care for you and believe in you, a very touching scene overall.