Most of my favorite fictional couples have a son. Not just a son among their other kids or something, but exclusively one kid, a boy. Why no girls? Rude.
John Crichton and Aeryn Sun of Farscape and their son Deke. Deke is like a sign of peace in the galaxy. He has pretty famous parents who helped secure peace between the Scarrans and the Peacekeepers. His existence in and of itself is hope for the future of earth. When he was still in utero he was just one big SYMBOL for the John/Aeryn relationship and the relationship between humans and Peacekeepers. But in the comic he is definitely a little person.
Howl Pendragon and Sophie Hatter of The Moving Castle series and their son Morgan. So Morgan must be the coolest baby ever. First of all he was born as a cat while his mom was also a cat and his father was a genie and they were all traveling with Abdullah. He was born as a cat. Morgan is ridiculously spoiled and terribly loved and a really funny little toddler.
Fox Mulder and Dana Scully of The X-Files and their son William. So William is totally going to save the world in a few years. That much is clear. According to that UFO cult he will finish what his father started and defeat the aliens. The poor thing doesn't even get to be raised by his parents, two of the coolest people in the world, but that fits the Chosen One motif so it's all good.
Lucius Malfoy and Narcissa Malfoy of Harry Potter and their son Draco. In an odd way they are by far the most normal family you will see on this list. There is not much to say about the Malfoy clan that has not been said before but I will say this. Draco must have been one pampered little child. Living in that manor with his parents and those peacocks for the first eleven years of his life...
Michael Cadogen and Caddy Casson of The Casson series and their son Carlos. Poor Buttercup, I doubt he will ever entirely shake that nick-name. He is the product of an entire book series of missteps and confusion between his parents. He is the best way to end a book ever. Authors around the world take note. You will never live up to the Buttercup Carlos Michael Cadogen Blues.
(Since these books don't have fan art I have used a picture of a sea lion. Carlos was named after a sea lion so it is appropriate.)
Desmond Hume and Penelope Widmore of LOST and their son Charlie. I love that family and all their potential. Although I was relatively fond of the end of LOST part of me wishes it could have just been the Hume Family Show forever. I think the creators of LOST got in over their heads with Des and Pen, they were just too amazing. They felt trapped in the background of the show. He's a lucky kid. His parents are amazing and he lives on a boat.
Remus Lupin and Dora Tonks of Harry Potter and their son Teddy. Of course Teddy doesn't get raised by his parents but they still had him for a while. I really like what JK did with Teddy, he is a sign of the new and better wizarding world. Of course he'll be an amazing person because look at his parents!
Will Turner and Elizabeth Swann of Pirates of the Carribean and their son William. The biggest plot hole of the last movie was Elizabeth. She could have just impaled herself with a sword and said no to death and joined Will's crew for all eternity. But then she wouldn't have had a son I guess, and then that would have messed with the pattern of my OTPs having sons so it's all good in the end.
So, Rory and Amy? You have a mission to fullfill.