Of course, Reader and Reader are an interesting couple in Calvino's If on Winter's Night A Traveler, even though their relationship is not my favorite. And I was listening to an episode of To The Best Of Our Knowledge a while back and they were discussing the potentially negative impact of the Bella-Edward relationship in Twilight, showing young girls that it's okay and actually desirable to have a boyfriend who sneaks into your room and watches you sleep, who is overly protective and warns you not to get into any trouble (and won't let you be friends with someone just because they are eternally enemies - ugh). So, while I think that their relationship makes for good reading, their relationship seems a little co-dependent to be my favorite.
I really like Scarlett and Rhett Butler in Gone With the Wind, because they're such a classic couple; and Henry and Clare in The Time Traveler's Wife, because their story is so heartbreaking but they really, truly love each other.
But, my FAVORITE literary couple is, by far, Claire and Jamie Fraser of the Outlander series. They are both individuals; they are independent, and they love each other completely and honestly. Their love is just beautifully written by Diana Gabaldon, and they are absolutely believable as a couple (and as individuals). I don't think I could've continued reading all of the books if it weren't for Jamie and Claire. They both get time to develop as characters, and then they have time to develop as a couple as well.