In Genealogy of the Holy War, Ethlyn and Quan are a Battle Couple who never argue and support each other in helping Sigurd (who is Ethlyn's sister and Quan's longtime friend). Promotional art shows them and their kids as a loving family.
Selfina and Glade in Thracia 776 are both knights. Selfina reassures Glade when he feels guilty over the deaths of his troops and Glade likewise when Selfina is still mourning the death of her friends Quan and Ethlyn.
Yuno and Zealot in Sword of Seals are another longtime Battle Couple who tried to retire and start a family before getting called back into service. Yuno's sisters both gush over what a good husband Zealot is; in Yuno and Zealot's own supports, they worry about the daughter they left behind but agree that they both need to stay in the field.
In Blazing Sword, Pent and Louise are another couple that joins your army. (Their children both feature in Sword of Seals.) Their supports are basically about how much they love each other and want to be with each other when the war's over. One of the rare non-Battle Couple happy marriages occurs with Dorcas and his NPC wife Nathalie. Her status as an Ill Girl drives Dorcas to banditry, but she follows him to talk him out of it despite her condition.
Kingdom Hearts has (in theory at least) Mickey and Minnie Mouse. Since they rule together as King and Queen, it's not unreasonable to presume they're married, although it's never explicitly stated that they are.
Prior to this they were married with children in Mickey's Christmas Carol, where they played the Cratchits; they also appeared to be married in a dream sequence in Mickey's Nightmare. A particular quote of Walt Disney's from 1933 tends to float around, stating that "In private life Mickey is married to Minnie..." Fans tend to either shrug this off or take it as canon; either way, the main consensus seems to be to keep them eternally courting as to not "spoil the illusion of youth."
Atrus and Katran of Myst, in contrast with their epically screwed up family in general. And if those two had paid more attention to what their kids got up to, the Stranger could have avoided twenty years of troubleshooting.
Saavedro and Tamra count as well (that is, before Sirrus and Achenar arrive on Narayan...) Sadly, it's never clarified if she survived/stayed single in those twenty years when Saavedro was trapped.
Cecil and Rosa of Final Fantasy IV, at least after the credits and in the sequel. The only primary couple in the main Final Fantasy series to date that has managed this, astonishingly. While some other pairs are implied to become this later, Zidane and Garnet of Final Fantasy IX most prominently, only Cecil and Rosa have officially tied the knot, which is what this trope is about.
In Final Fantasy VIII, Cid Kramer and his wife sorceress Edea were a happy, loving, and mutually devoted couple until Ultimecia's possession of Edea forced them to separate. Once they're reunited after the end of the game's second disc their marriage is as strong and supportive as ever, with Edea describing Cid as her knight.
Final Fantasy XII had Ashe and Rassler and their Perfectly Arranged Marriage. They share a joke in the prologue about how everyone thinks they're marrying for political convenience when the reality is they're in love. Since he dies in the opening credits, Ashe becomes a Crusading Widower for the bulk of the game.
Wakka and Lulu from Final Fantasy X. Their marriage is a sign they've moved past their angst from the first game note the death of Wakka's brother and Lulu's former boyfriend and indeed they are happy and parents. One such mission in the sequel is searching for a sphere containing information about Wakka's parents which Wakka is looking for because he wants to use it as a model for what a good father should be.
John and Abigail Marston of Red Dead Redemption. Even though Abigail is held hostage for most of the game, John turns down the advances of many women, and does everything within his power to get his family back. And eventually he does.
Part of the Harvest Moon experience is the player character becoming Happily Married to the bachelor/ette of their choice. Supposed to be a small part of the game, but Popularity Power means that it's grown in importance as the series continues. That aside, within the games themselves are several (dozen) NPC couples, the majority if not the entirety being Happily Married.
Subverted in Harvest Moon DS (Cute) where, when you talk to the rival couples after marriage, all but one couple seem to voice doubts about the marriage to the player.
Umineko is impressive by managing to have two very unexpected Happily Married couples; Eva and Hideyoshi, in a family full of internal squabbling and backbiting, manage to be good, loving spouses. She snaps as soon as he dies, showing that the marriage is really Eva's rock concerning her sanity. And secondly, and doubly impressive is Battler/Beato, counting as a bizarre combination of Happily Married and Unholy Matrimony; Battler is The Hero, and Beatrice is The Chessmaster. Everything suggests that they honestly enjoy challenging each other, though, and it might just be a pillar of their happy marriage.
King's Quest: Graham and Valanice seem to be doing pretty well for themselves, Alexander and Cassima also seem to be doing okay, Cassima's parents seem happy, and it's pretty much assumed that Edgar and Rosella will go here... eventually. In the Fan Remake of King's Quest II: Romancing The Throne Caldaur and Lavidia, Count and Countess of Kolyma also are still quite in love.
Khalid and Jaheira of Baldur's Gate. Sure, Jaheira is bossy around him but their marriage is a happy one. She also cries when Khalid dies. The player character can also be married with either Jaheira, Aerie and Anomen.
The world of Dragon Age seems significantly more accepting of extramarital affairs than a normal medieval setting, so the only romantic pairing in either game in which the player ends up getting married is with a female Human Noble Warden and Alistair in the first game. (Theirs is, however, an extremely happy marriage; the epilogue states that Alistair openly adores his wife.)
Guybrush Threepwood and Elaine Marley as of the end of Curse. Despite Elaine's arguably superior intellect and competency, she always trusts Guybrush. The only time their marriage is remotely threatened is in Tales, when she falls under the Pox of Lechuck and he spends his entire adventure with another woman, but he never turns away from Elaine, and by the end of chapter four it's clear that she'll do anything for him.
The happiest married couple in the Ace Attorney series is the unlikely pairing of Ron and Desirée De Lite. She's a badass motorcycle chick and he's a nervous girly-man, but they still love each other greatly, and Ron is willing to put himself in harms way for his wife.
Almost every Dynasty Warriors and Samurai Warriors husband/wife team is a good match between people who do care about each other, often ignoring both history and the source material, though Hideyoshi is still a bit of a lech and Nohime is a very mentally disturbed woman.