My initial thought: I have no idea.
This seems like a rather romancey question, and since I rarely read books for the romance, or think in terms of couples, I don't have a good response to this one. Weirdly, I can think of a few from other media, such as Derek Wildstar & Nova, Kitty & Peter, or Deckard & Rachel. But in genre literature, a favorite does not come easily.
My first response? Jaxom and Ruth, the focus couple of Anne McCaffrey's The White Dragon. Both put-upon by life (Jaxom an orphan, Ruth a runt), they end up being the outsiders who win the day. They love each other, go to great lengths for one another, work well together, and their bond is strong enough to see them through some rough times and gives them the sand to be heroes. They are not trusted, sometimes overprotected, and few seem to understand their connection at first. But they overcome social convention and long odds to contribute significantly to the wellbeing of their world.
I read the series in high school my sophomore year, and then re-read the third book several times, because I loved the two of them together. Whelan's cover, with all the little fire lizards hanging around, is as clear in my mind as the day I first set eyes on the book. Those fire lizards were for me an odd validation of Jaxom and Ruth's love, of the projection of it to others who were often ignored and disparaged. And their relationship was very straightforward; as Ruth put it: I am the white dragon. You are my rider. We are together. But they were not just for each other; their relationship was crucial to Pern. It made more sense to me then, and still does now, than a lot of the romantic unions people cite as their favorite.