If you end up taking Banjo or Kazooie far apart from each other in Banjo-Tooie, they will end up whining about missing each other. And considering how much they argue, their differing personalities, and the fact Banjo often uses Kazooie as a weapon, this means A LOT.
In BoxxyQuest: The Gathering Storm, Anonymous and Til spend most of the game snarking the hell out of each other, but there are a few times near the end when theyre able to open up and express their true feelings. The biggest example is probably the scene just before the final fight with STORM, when Til apologizes for misjudging Anon when they first met, praises his hacking skills, and comes this freakin close to confessing before she stops herself.
In the end of Chibi-Robo!, after Chibi and Mr. Sanderson have saved the house from the Spydorz, Mrs. Sanderson rushes to his side, tackles him to the ground and, and gives him a big smooooch! She considers the argument they've been having over the entire game to be over.
Despite Morrigan frequently expressing annoyance at the Dog in Origins for leaving dead rabbits in her pack because he thinks she needs to eat more, when the Dog happily bounds up to greet her for the first time in two years at the end of Witch Hunt, she greets him as an old friend and displays one of her very rare smiles.
Happens when Hawke is romancing Merrill as a rival.
Really, any rival romance is like this. Extra points go to the Anders rivalmance.
Anders: I swear I don't know whether to kiss you or kill you.
In Fantasia - Requiem of the Abyss, Cain and Valen spend most of the time insulting each other. Cue "awwww" when he says that he loves her. On a less romantic side, Oswald and Valen as well. Stern daddy admits he cares about daughter's safety.
Erk and Serra in Fire Emblem: The Blazing Blade if you pair them up. Their A support has him asking her rather roughly why does she tag along with him when she hates him so much... but Serra unexpectedly says she's trying to take care of Erk so he won't neglect himself to death. Then he replies that he's trying to protect her because he believes nobody else would do it.
Grand Theft Auto V: Michael and his son Jimmy. While Jimmy openly calls his father a Jaded Washout with a "completely fucked" moral compass and Michael repeatedly calls Jimmy a fat slob who leeches off of his money, Michael tends to level with Jimmy and Jimmy outright states he's worried Michael is gonna get himself killed.
The entire DeSanta family, really. Michael doesn't understand his kids at all and his attempts to bond with them usually don't go well. But the second either of them are in danger, Michael will rush in to help them. Michael and Amanda are constantly at each other's throats, but after a period of separation Amanda and the kids begin to miss Michael. After they reunite, at the end of an intense family therapy session, Michael tells Amanda that he'd kill her if she ever reported him to the police, in a tone that makes it sound like he means. Afterwards, the two have a civil conversation on the way home where Amanda tells Michael to not get himself killed while he takes care of his business.
Michael and Trevor. The two fight about everything, from how to approach a job to Michael's decision to retire. Trevor is extremely bitter about Michael giving him up to the police as part of a deal with the FIB, and becomes homicidal when he discovers that their partner Brad was killed, instead of arrested like Trevor thought. Yet, no matter how bad things get between them, they can never stop caring about the other's well being. To borrow a quote from South Park, they're best friends whether they like it or not.
Guild Wars: Eye of the North has Gadd and Vekk at odds with one another, Gadd criticizing Vekk for too much concern with safety and for his comrades while Vekk criticizes Gadd for putting his pursuit of knowledge ahead of everything else. When Gadd dies while preparing a golem Vekk collapses in tears because no matter how much they argued, they were still father and son.
Nick will spend all of Left 4 Dead 2 insulting his comrades, but if any of them die, he may say something about how he'll miss them, except for Ellis on some occasions.
Mortal Kombat X: JohnnyCage and SonyaBlade are this to a T, especially on her side. Especially seen in the flashbacks, where Sonya is easily resting her head in Johnny's arms after he had just defeated Shinnok, or her immediate reaction to seeing him get stabbed is a severe beatdown on Quan-Chi, topped off with a vicious stomp between his legs. And despite a rather bitter divorce during the timeskip between 9 and X, when Cage is feared killed in the comic, Sonya frantically begs for him to respond, and is surprisingly gentle in dressing his wounds. Pretty much all their more heartwarming interactions in MKX boil down to this trope.
Radiant Historia has one and only one moment where Stocke and Raynie share affection, during a Non-Standard Game Over, and it's a doozie. In which they give up fighting to live in peace together for an entire year before the world ends together. Stocke uses the White Chronicle to go back in time to tell Raynie he can't give up fighting, and instead makes The Promise.
Radiata Stories has Jack and Ridley who initially can't hold a conversation that doesn't involve insulting each other. After a mssion goes wrong, Jack devotes himself to protecting her and she becomes affectionate in return.
Possibly subverted in the end of Ratchet: Deadlocked, where the commentators Dallas and Juanita, having verbally attacked each other all through the game, end up getting married, though this was a result of deception on Dallas' part. They then go on to star in their own TV show, where Juanita attempts to kill him in every episode.
In Red Dead Redemption and Red Dead Redemption II, we have John Marston and his girlfriend and eventual wife Abigail. When she is first introduced late in the first game, the first words out of her mouth are "You useless hillbilly piece of shit!" before berating him until, eventually, she calms down and embraces him. Afterwards, the two continue to enjoy sniping at each other, but the fact remains that the two care about each other immensely and would continue to do so until John's Heroic Sacrifice to save her and their son. 2 demonstrates that their relationship wasn't always so relatively rosy, as John was loyal to Dutch to a fault, even though it meant putting himself in constant danger and carrying out morally dubious (if not outright criminal) acts for him. He was also initially unwilling to accept that their child was actually his, although in time, he would come to accept his son and start making strides to break off from Dutch's gang and start a new life for his family.
Kaltos and Charlotte from The Spirit Engine 2 if you have them in the same party. Despite constant bickering and insults, they suddenly turn out to love each other near the end, even though there's no indication of it whatsoever.