The end of A Pinky and the BrainChristmas counts when Pinky gives Brain the world for Christmas. (Sort of - it's a little globe on a keychain)
The scene right before it is even better — Brain is just seconds from bringing his plan to total success, until he turns and sees just how sad Pinky is at not being able to give his letter to Santa Claus. Right then and there, Brain effectively decides that if Pinky can't get what he wants, then neither will he. Of course, it wasn't so much the letter itself as it was the contents of that letter. Brain initially passes it off as some stupid letter Pinky wrote. When he actually reads it, he realizes that Pinky was writing to Santa about how great a guy the Brain is, yet no one respects him, and that Pinky wished for Santa to give the Brain respect, and maybe even the world to go along with it. Who knows if Brain was tearing up more out of Pinky giving him the respect he so desired or the realization that he acted like a Jerkass towards Pinky, yet Pinky still wrote all that, but, er, it's just the fluorescent lighting....
"Dear Santa, hello, hah hah, narf! This year Santa, I ask for nothing, but I wish to tell you about my dear friend, the Brain. He is honest and very hard working, and only wants what's best for the world, but he gets no reward. He is only greeted with defeat. He never gives up, but I know it must be very hard, so please, take anything that you have for me and give it to my best friend in the whole world, the Brain. Love Pinky. (PS. By any chance do you have in that big old bag of yours the world?"
This troper is an embittered jerk who kept a straight face throughout WALL•E, and has never seen Pinky and The Brain before. That entry made her tear up right there. That's how touching it is.
What makes this moment all the more touching is that for the very first time, Brain realizes how abusive he's been to Pinky. Even though he doesn't speak, the tears in his eyes say louder than words the one thing Brain is thinking: He's my only friend and I made him cry.
More to the heartwarming factor, that wasn't the only time Brain kept disregarding Pinky's letter, it happened about four other times before that.
And to take it up to eleven (it being Brain's guilt and the heartwarming mood of the moment), despite tearing up uncontrollably, Pinky refuses to defy Brain and follows his instructions to activate the device.
Brain: I command you to... (Beat) have a merry Christmas, everyone! Have a merry, merry Christmas! Joy to the world! Yes! *cries, smashes machine*
Pinky said the letter was very, very important, whose name was mentioned over and over in the letter? Therefore, who is very, very important to Pinky?
The ending of the episode where Pinky succeeds at getting Brain the world for his birthday — after Brain screws it up himself (of course), instead of getting angry, he quietly says, "I don't deserve a friend like you, Pinky."
"Two Mice and a Baby." Apparently Kal-El spent a few days with a pair of lab mice who grew to love him. In the end, they decided to give him back to a pair of human parents as they realized he would have a better upbringing there.
The scene where they give him to his human parents moves Brain to tears.
Brain: My eyes...they're leaking!
Pinky: No Brain, you're crying.
Pinky himself is a heartwarming character. He completely respects Brain's position and often affirms and cheers him on. Many episodes, such as That Smarts show how he doesn't mind how useful he is in taking over the world, because he values his friendship with Brain a lot more.
Pinky: (sniffling) Being smart isn't any fun...Brain doesn't like me.
To some degree, Pinky is an Audience Surrogate. He sympathizes with Brain and so desperately wants something to go right for him. The above example pretty much shows his vehemence in trying to even get him a Christmas present, even listing all of Brain's redeeming qualities that make the audience empathize with him. He wasn't crying because Brain yelled at him, he was already in tears, because he so wanted to Throw Brain A Bone and fate had so cruelly robbed him the chance.
In "That Smarts" when Brain believes it's Pinky's fault that their plans never succeed, he never even considers abandoning Pinky.
Brain almost always refers to his inventions as "our invention [he and Pinky]", and says "The world will be ours!"
And seems to hold to this the odd occasion they actually succeed at something, when he and Pinky manage to drive people off the Earth with their own artificial planet for example, he is shown enjoying the high life with Pinky (which is probably just as well, since he soon finds the outcome to be rather lonely).
Brain always acknowledges Pinky's intentional and serendipitous acts that contribute to his plans.
In "Welcome to the Jungle" Brain finds himself completely unable to adapt and becomes the load with Pinky taking care of him. Then the two find themselves in the hands of a delirious Snowball and a group of far flung tourists who tie them both to stakes and are about to fry 'em alive. Pinky gets knocked into some quicksand. After spending the entire episode being unable to help, Brain suddenly finds his inner wild, breaks the ropes, defeats snowball and saves Pinky. Thing is he only did all of that because Pinky was in danger in the first place.
Pretty much the entire episode of "The Family That Poits Together, Narfs Together".