Any match where NicePeter and EpicLloyd are on the same side. There's something nice about seeing them working together.
Vince Offer coming in to take over for Billy Mays after the latter dies. His utter schooling of Ben Franklin can almost be seen as avenging him - ironic when you consider their real life hostility.
Randy Savage tagging in to take over for Hulk Hogan after Kim Jong Il fires a rocket at him. The video was uploaded a few months before Macho Man died, while the two had been trying to patch things up after their decade long animosity towards each other, one can view this as a sort of burial of the hatchet.
Not to mention that instead of two separate screens, the two dance together on the same screen at the end.
More than any of the other videos their interplay comes off less like a rap battle and more like a heated argument between friends, switching between lines rather than verses and often speaking while standing next to each other. In fact, Bill's Villainous Breakdown at the end could be read as poorly handled grief for losing Steve.
Dumbledore flying away with Gilderoy at the end of his battle with Gandalf.
At the end of the battle between Peter and Lloyd, it looks like Peter is about to pull a Rage Quit and completely end the rap battle series... then, Kassem G swoops in and gives something of a Rousing Speech that convinces him to make a second season.
A meta-example: in the battle between the Wright Bros. and the Mario Bros., the Wright Bros. are played by Rhett & Link, whom Peter and Lloyd have stated were a huge inspiration to them.
The Wright Bros. VS Mario Bros. battle has both pairs of siblings working together flawlessly, showing the true bond between the brothers on both sides.
There's a subtle moment in Obama vs. Romney: Obama's line about having his fist kiss Romney's face comes right after he insults Obama's wife.
Doc Brown coming to the defense of Marty McFly.
Batman shows clear displeasure when Robin joins in to rap with him, before finally interrupting him with a smoke bomb. In contrast, Holmes actively includes Watson in his own verses.
Santa's elves finally outright stating that they are not Santa's slaves and are in fact the friendly, mystical helpers they are supposed to be portrayed as...with a bit of Smack Talk thrown in, of course.
At the end of their rap, Adam and Eve apologize to each other, implying it was just a bump in an otherwise happy relationship.
Dr. King is obviously very happy to be meeting Gandhi. He says he admires how he broke the British power, and even gives him a big hug during his last verse. Even if the feeling isn't mutual, it's still a sweet gesture.
And, even though Gandhi doesn't feel happy meeting Dr. King, they still dance together at the end, indicating they're both actual friendly enemies.
They're not just dancing, even—Dr. King is dancing while Gandhi is cheering him on.
In the third installment of Darth Vader Vs Adolf Hitler, Boba Fett joins in for 8 seconds (all of which were golden) before getting shot by Hitler. Not only was Vader actively enjoying Boba's rap, but shows visible anger when Hitler shoots Boba Fett, and seconds later, kills Hitler, mid-rant, as revenge. No carbonite freeze, no Rancor pit, he finally has had enough, and just straight up Darth Maul's him.
Their video thanking the audience for all their support, to the point they got nominated for a Youtube music award!
Pablo Picasso, portrayed as a Grumpy Bear, lightens up when he mentions his pet dog, Lump.
JP Morgan telling off Ebenezer Scrooge for his greed and misanthropy, ending with, "Your greed is the curse that's going to tear you apart! What good is a purse, if you're poor in the heart?" Given that JP Morgan was a noted philanthropist in addition to being one of the richest and most powerful men of his time (not to mention the man solely responsible for preventing the united states banking system from collapsing in 1907), while no saint, he was the equivalent of Uncle Pennybags compared to Scrooge.
A bit meta, but the way Peter describes how he and Lloyd write the lyrics for the rap battles shows how passionate they are about what they do.
Peter: Writing is sometimes hard, and sometimes easy. It just depends. It's like—If you're like, a mom, and you have like nine babies. Some of them are labor for 40 hours and some of them are labor for like 20 minutes. They're all different, but we love them all the same.