In Super Robot Wars Reversal, the Big BadDuminuss decides to escape defeat by the heroes through Time Travel via the device built specifically for it after kidnapping the protagonist's Sidekicks. Upon activation, the device explodes, having been earlier sabotaged by one of the sidekicks, because he wasn't going to let Duminuss have its way. Horrified, its homunculi run to their master and do the only thing they can think of to ensure its survival. Realizing it cannot stop the three homunculi from sacrificing their souls to save it, Duminuss offers them a boon: when it destroys the heroes and remakes them, it will be in any way, shape or form they desire. The homunculi accept and promptly sacrifices themselves to regenerate Duminuss' wounds. Despite being nothing more then mindless, soulless husks, their bodies stay by Duminuss, protecting it for the rest of the battle with their lives.
But at least it gives us another set Heartwarming scenes, notably Axel Almer and his HeelFace Turn event and his eventual speech towards Lamia Loveless, declaring that he finally would consider her a human being (and this is coming from a guy who used to make fun of Artificial Humans).
Later on, Lamia returns the favor when Axel expressed confusion on what to do, telling him to find his paradise. Axel promised to let her be the first to know if he ever finds one. Aww...!
Beforehand, there's also the fact that despite what Duminuss's homunculi did to them, when Despinis is about to get Killed Off for Real by Dark Brain, Raul and Fiona Gureden speed to her protection, telling her that she doesn't deserve to die and let her join them in the fight against it. Original Generation Gaiden ends with the Gureden siblings adopting Despinis into the family and by the Second Original Generation, she's overcoming her shyness, if only little by little. Aww....
During the Earth Cradle scenario in Original Generation 2, Mai Kobayashi has a combat dialogue towards Ouka Nagisa. It's something like "For Latooni's sake, I'm going to disable your mech!" Never let the love triangle they're in make you assume that the two aren't good friends.
Though more poignant, before his death in Alpha 3, Shinji and Gendo Ikari actually had a heartfelt talk. Shinji asserts in a normal way that he's his own person and he'll choose his destiny. And guess what Gendo does? Admits that he's wrong, and he's very proud about Shinji making his own decision, even if he's not going to live on to see that, and he's sorry for being a horrible father. It makes Gendo appearing as a spirit during the final battle against Keisar Ephes more meaningful.
As an extension of this, if certain conditions are met in Original Generation 2, Excellen tweaks the "family" dialogue a bit: she instead wants twin daughters, to which Kyosuke correctly guesses one will be named "Alfimi" and the other "Lemon", after her Alternate Universe counterpart.
At the epilogue of the Second Original Generation, likely as a Call-Back to the above, after all their friendship and efforts fighting together, the ATX Team swear to find and resolve Ariel Org'slongevity problem. Excellen chippers in with "Isn't that great, Kyosuke? Ariel can be our daughter!". Kyosuke just smiles at the remark.
Becomes painfully Harsher in Hindsight in another way: Her voice actress, Yuko Mizutani has died from cancer. Excellen will always be Excellen, but she'll never sound the same again.
At the end of 2nd Super Robot Wars Original Generation. Axel parts from Kyosuke and Excellen.
Lamia : What are you going to do now, Captain Axel?
Axel: Let's see. The Cross Gates bother me a bit, call this fate maybe. But I don't see myself going with the Steel Dragon Battle Group.
Rästel: Then you're welcome to come with us. We already have a place for the Soulgain, after all.
Touma: Mr. Axel, I'd really like to train with you again.
Axel: Fine. Prepare yourself.
Excellen: Alfimi sweetie, are you going to follow Axel?
Alfimi: Yes. We're bound by firm and solid ties, now.
Axel: Unsavory ties to me.
Alfimi: Your mouth says that but...your heart...
Excellen: What a great combination. Take good care of Alfimi.
Kyosuke: See you later, Axel Almer.
Axel: Shit happens when I see you. I wonder what it'll be next time.
In The Moon Dwellers, upon hearing that Al died during Team Jelba's escape, Shu claims that it's time to fulfill his promise and defend Earth.
Meta example: In an interview conducted for the Famitsu preview of Super Robot Wars BX, members of the staff explained their reasons behind their choices for the roster. One of them is to bring back some old friends.
In most of the games that included Martian Successor Nadesico: The Prince of Darkness, it really warms the heart of most anime fans that Akito, after being disillusioned with Gekiganger 3 due to its plot being used as a basis for the Jovian Lizards to ruin people's lives and currently in his Empty Shell self, actually revisits the Gekiganger once again and then eventually admits that, putting the whole "having it's overall message twisted by the Jovian Lizards to better fit their blind hatred and desire for revenge against Earthlings" thing aside, it's not that bad. He pretty much was given the chance to rekindle the love for the Gekiganger anime, and it was sweet.
W also ups the ante that not only Yurika recovered from her catatonic state, Akito is seen recovering his sense of taste.Throw the Dog a Bone doesn't even describe what it is.