Dr. Watson and Sally SparrowMeet Cute in "Watson and Sparrow" and go on to marry in the next episode. They remain very in love and very devoted to each other, especially as Sally gives up her life in the 21st century to be with Watson at the close of the 19th. Sally gives birth to a daughter who turns out to be a Time Lord, and the couple eventually have more children. Even Holmes, in the end, is grateful for Sally and the children, attaching himself wholeheartedly to his best friend's family.
Beth Lestrade, on the other hand, has no less than a Trauma Conga Line in her relationship with Sherlock Holmes, but she earns her happy ending and marries him before returning to her own era. When the couple are reunited at last, they still have some issues to iron out, but their long separation has only deepened their appreciation for each other. Beth has commented that they will probably never get off the honeymoon, and both are perfectly fine with that. Now, They Fight Crime in the 22nd century, particularly dealing with the clone of Professor Moriarty.
In Marks of Time, Meredith and Gilorn. Also, Caleniel and her husband. The worst moment is a brief argument between Meredith and Gilorn in chapter 2, but they quickly apologize and forgive each other.
Fleur De Lis and Fancy Pants in Of Lilies and Chestnuts. When Fancy learns that Fleur is infertile, his first act is to comfort her in her despair for a few hours and suggest adopting a foal so Fleur can salvage a glimpse of her dream. Fleur adores her husband in return.