So, we have 9 and Rose, 10 and Rose, 10.5 and Rose, Amy and Rory and Madam Vastra and Jenny. We could also include the Doctor and Idris, of course.
While our Silurian private detective and her wife are just brilliant and have so much more to give us, for me, the best couple has to be Amy and Rory. We've seen their relationship develop, it's a partnership of equals, they love each other incredibly and that love has been well and truly tested. I don't think for a moment, though, that they would have actually split up. They would surely have talked it through before it got to that stage. Even if Amy had thrown him out, Rory had the emotional intelligence to get to the bottom of it.
As for 10 and Rose, it was a really soppy love story but it was pretty one dimensional and only really there to make us cry when they were separated at the end of Season 2.