In the Lab Rat tie-in comic, it's revealed that Chell was chosen as a test subject by Doug Rattmann, despite her file listing her as being rejected. Why? Because, according to her file, Chell is abnormally tenacious. She never gives up. Ever.
Wheatley is a huge Adorkable mess. Friendly, chatty, and charismatic, he immediately regards Chell as an odd, but trustworthy, friend. He rescues Chell from her room and guides her to the Portal Gun, and also helps Chell escape from GLaDOS and create a trap for her. He's the first ally Chell has really had in this crazy place...until his Face–Heel Turn, of course.
But even after he is sent into space, Wheatley becomes guilt-ridden about what he did, and wishes he could apologize to Chell for it. In the end, Wheatley felt the same way about Chell as she (presumably) did about him.
The fact that, after everything that happens in both games, after all the hell that GLaDOS and Chell have put each other through, after stopping Wheatley from letting Aperture Science go up in a nuclear fireball, GLaDOS honestly, truly, no strings attached, lets Chell leave.
In the last moment, as well, GLaDOS sends up an old friend to join Chell as she leaves for the surface: the Weighted Companion Cube! And it's the same Companion Cube from Portal, not the newer design from 2. The old design is just barely visible, beneath the chars from being in the incinerator.
GLaDOS pulling Chell back from the moon portal. It's especially heartwarming since, despite her insistence otherwise, she could have finally accomplished her original goal of killing Chell (by letting her fly off into space), and yet she chose to save her life and set her free instead.
And there's also GLaDOS's genuine relief and happiness to see Chell is okay after pulling her back from the moon.
Furthermore, look at the Earth from the Moon: the oceans are blue and when Chell emerges on the surface its in the middle of a fertile field. As Portal 2 is set after Half-Life 2, this means the Combine were ultimately completely repelled and the world has been restored.
The credits song in Portal 2 has GLaDOS sing that she no longer wants to kill Chell and lets her leave, even though she calls her fat...again.
Debatably, GLaDOS defending Chell against Wheatley's insults—the exact same insults she herself used earlier. "Look at her, you moron. She's not fat."/"And what, exactly, is wrong with being adopted?" It's arguably spoiled when she later says: "For the record, you ARE adopted, and that's terrible. But just work with me here." But it's possible to interpret that less as a barb at Chell and more just saying that it was terrible that her birth parents gave her up.
Any time GLaDOS acknowledges you as a worthy rival, even if it's to spite Wheatley. "You didn't do anything. She did all the work."
GLaDOS's response to Cave Johnson's pre-recorded last words:
"Goodbye, sir."
The fact that her response was so automatic and instinctive; some of her small talk with Chell suggests that she doesn't completely remember Cave, but that response implies that something inside her is still loyal to the man she/Caroline loved and admired.
Earning the "No Hard Feelings" achievement. The Oracle Turret's quiet, desperate plea of "I'm different" and its subsequent thankfulness upon being rescued really make the moment.
The ending to the co-op campaign. Atlas and P-Body succeed in opening the giant vault, and inside are thousands upon thousands of human test subjects in cryogenic stasis. Even though the only purpose to finding them was that so GLaDOS could resume her human testing, and it's fairly obvious that most of them are doomed to die during said testing, the fact that GLaDOS herself is so unbelievably overjoyed turns it into a strange heartwarmer.
GLaDOS: You saved science.
The little space-obsessed core at the end of 2 gets his fondest wish, and he sounds absolutely overjoyed. Luckily they left out some of his Dummied Out lines which show him being overwhelmed with space and wanting to go home, or it could have been more gut-wrenching.
During the ending credits of 2, GLaDOS sings about not needing anyone anymore (though she could easily be in denial), and that she might delete Chell from her memory. The lyrics for one line read "REDACTED," and the sound becomes a bit garbled, but the words are still easily audible: "When I delete you maybe/I'll stop feeling so bad." Plus, the subtitles (if they're turned on) give the line away, anyway. GLaDOS, you big murderous softy!
Part of the ending to Portal 2 where all the turrets stare at you as you rise to the surface...and they all sing the most gorgeous song. GLaDOS may claim she still hates you, but the other beings in Aperture Science Testing Facility make it very clear that they are grateful for everything you've done for them. (Even if it involved you knocking a few of them over.)
It gets even more heart-warming when you look at the English translation of the Italian lyrics:
Dear beautiful, my beautiful darling! My child, oh Chell! [pun: "oh heavens!"] For I hold her in esteem... For I hold her in esteem. Farewell to my dear!
My dear girl, why do you not walk away? Yes, far away from Science. My dear, my dear girl? Ah, my beautiful! Ah, my dear! Ah, my dear! Ah, my child! Oh dear, my dear...
During the final test for the Hard Light Bridges portion of the Co-Op Campaign, Atlas and P-body are faced with a problem with a relatively simple execution: cut the bridge so that they fall into a portal and get flung onto a catwalk. As it turns out, the velocity can cause them to overshoot the catwalk and fall into the abyss below. What do they do? Use each other as a wall so they stop right on the mark. Shortly after, Atlas hugs P-body, cementing their already developing friendship.
The trailer has a similar hug moment: Atlas inadvertently smashes P-body, who is then rebuild just behind him, showing that neither can actually die. P-body waves calmly at his friend and Atlas hugs him because he's just so glad he's alright.
A small one compared to the others, but in co-op, the player playing as P-Body can hear some unique dialogue that only they can hear after completing Course 4, Chamber 1. It's funny as well, since the player playing at Atlas never hears this.
"Test chamber completed. In the interest of - [FADES OUT] [FADES IN] I am now talking to you privately. Do not tell your teammate. Just between you and me? You're doing very well. [FADES BACK IN] One hundred and seven."
Just the fact that GLaDOS waits until Chell wakes up and it can be confirmed that she's all right before she deletes Caroline. We don't know how long it took Chell to wake up, but it certainly was long enough to fix the chamber. It had to have been at least several hours since it's night when you defeat Wheatley, and day when you leave the facility.
Wheatley's apology. From space.
The song "Love as a Construct" from Portal 2 for the Companion Cube is very sweet and oddly touching, in its beepy electronic way.
Yes, that song's associated with love in this game, it's so sweet how the Companion Cube hums it just for you! And if you listen carefully, you can also hear it being played (very softly) as Chell is losing consciousness after GLaDOS pulls her back in.
On a related note, Exile Vilify is the most heartwarming thing in the entire Valve body of And I Must Scream work. Just imagine it playing at the end of the Lab Rat comic, as Rattmann peacefully goes to sleep...
Listen to the end song, and listen carefully. Notice a slight difference in the two last "that's what I'm counting on" parts and the very end of the song? Notice how it sounds like two voices singing together?. That's because it is. It's not just GLaDOS singing there... it's GLaDOS and Caroline!
Another from the ending song: "Under the circumstances I've been shockingly nice." It's passive aggressive snark in context, but it also makes one realize that GLaDOS really was much nicer in the second half than one would really think her capable of being.
Someone made a live-action film, which is set after the original ending of the first game. At first, it just seems like it's about Chell having GLaDOS flashbacks and trying to survive, but then she finds the cake book and sheds tears of joy. She spends the rest of the movie baking cake. Even better is what she writes on her wall.
"I get to have some cake today! The cube is watching me. I hope it's proud to see me now, Outside, Alone but free!!"
The ending of the new DLC "Art Therapy" co-op course, where GLaDOS adopts the baby birds. Even though the scene is tinged with the same abrasiveness and fridge horror GLaDOS usually brings to social interaction, her bending down over the incubator as a doting mother is very sweet...even if the insinuation of the scene is she has insidious plans involving them.
Look at those cold avian eyes. Those talons. Those razor-sharp beaks. You're little killing machines, aren't you? Yes. Go to sleep, my little killers. Mommy's got a big day for you tomorrow.
Before that, GLaDOS congratulating Atlas and P-Body for shooing the bird out of the facility. She seems genuinely proud of them.
Nice hustle... kill machines.
Chell running into her old science project. It might very well have been the last thing she actually got to do in her normal life. And now, all those years later, after being put through hell, Chell sees her little potato again—and it's well on its way to becoming its own ecosystem. There is no way that didn't cheer her up at least a little bit.
Cave Johnson's pre-recorded message where advises the homeless test subjects to not waste the sixty dollars they'll be getting later. Granted, the message is superficially just as insensitive as any of his others, but there's literally no reason for him to have recorded this besides being, on some level, concerned for his test subjects' well-being.
Rick the Adventure Core is one of the only people to unconditionally compliment Chell. Even though he is a sleazeball, it's very cute how he straight-up calls her beautiful upon seeing her for the first time.
The ending of Portal 2 has Chell emerging into a huge field of wheat with a beautiful blue sky above her. How is this heartwarming? Portal takes place in the Half-Life universe. And considering how bad the ecosystem looked in Half-Life 2, the state of things now certainly seems to suggest that the Combine were defeated.
Two of the pre-recorded messages from the announcer from the first chapter are directed at any survivors of a post-apocalyptic world who happen to discover the facility, welcoming them and telling that "testing is the future, and the future starts with you!" Another earlier one uses the phrase "when society has been rebuilt." There's something really heartwarming about Aperture's boundless optimism, especially in regards to what they assumed would be a post-apocalyptic world.
There's also this bit. Never has Ragnarök Proofing felt so uplifting.
Announcer: Well done. The Enrichment Center reminds you that although circumstances may appear bleak, You Are Not Alone. All Aperture Science Personality Constructs will remain functional in apocalyptic, low power environments of as few as 1.1 volts.note Which is the plot's justification for GlaDOS being able to function attached to a potato.
In the Perpetual Testing Initiative DLC: In one of the alternate dimensions, a sick boy named Timmy speaks to the player asking him to finish the test so he can feel better. The boy died shortly after, but Cave Prime and his team kept monitoring him and were all virtually pulling for him.
A fan-made video/song called This is Aperture (set to the tune of This is Halloween) has this line:
Turrets: "Our dear Chell is master of the Portal Gun, everybody help her in her flight."
