George and Lorraine McFly at the end of Back to the Future once Marty fixed the change he made to their past.
Given Lorraine's rant to Biff in the sequel, she and George had been happily married in that alternate universe as well, before Biff had George murdered. In the third movie, we see that Seamus and Maggie McFly were happily married as well.
In the end, in Who Framed Roger Rabbit?, it turns out that Roger and Jessica are Happily Married. (Even Sickeningly Sweethearts.) What does Jessica see in him exactly? When asked that by Eddie Valiant, she replies, "He makes me laugh."
The Little parents in Stuart Little, to the point where they finished the other's sentences. The moment they couldn't tell what the other was thinking led to slight panic, but all got resolved.
Jack and Marilyn Mickler, in Don Juan DeMarco. It gets even better as the title character's example works its magic on Jack's libido.
Alejandro and Elena in The Legend Of Zorro for the most part. They do split up for awhile, but that was mostly because Elena was blackmailed into splitting up with him
The parents in A Christmas Story. Not even the legendary "Battle Of The Lamp" can permanently derail them.
Undercover Blues: Despite a few disagreements about, e.g., taking the baby into dangerous situations, Jane and Jefferson Blues are one of the finest examples of Happily Married to be spotted in an action film. Their easy camaraderie is an enjoyable counterpart to the danger they're facing.
Mike and Jackie Flaherty from Win Win. Their relationship can get harried, but it's ultimately a loving and commited one.
Donald and Tim in the Donald Strachey mysteries are this right from the start, and they're adorable. Not that they don't have their problems, particularly with Donald's dangerous and time-consuming line of work, but that's life.
Celia and Johnny in The Help. All Johnny wants from Celia is for her to be happy. He doesn't care that she can't cook, properly take care of their house or that she had multiple miscarriages trying to give him children. Their first scene together where Johnny sneaks behind Celia and pulls her in close establishes their relationship pretty well.
Greg Kinnear and his wife in The Matador are happily married and their relationship is never at stake.
Andy Knightley from The World's End. Or so he claims. He's actually been having major difficulties as of late, although they get resolved by the apocalypse.