11 and River: Amusing flirting but that's about it. I didn't buy them as an actual couple for one minute.
Amy and Rory: I still think Rory deserved better, but Amy did eventually grow as a person and they ended up being a great couple.
Martha and Mickey: There was potential there and they could have been an awesome couple... unfortunately we never got to see any of the lead up to them getting together, so it really does feel like the writers shoved them together just for the sake of it. (Come on Big Finish, where's our Martha Jones, Freelance Fighter series? Fill in the gaps for us.)
Bill and Heather: Were these two even in a relationship?
Jenny and Vastra: Nice couple most of the time, but Vastra did seem to treat Jenny more like a maid than her wife sometimes.
Jackie and Pete: Probably the most realistic depiction of a relationship (at least the N-Space version of Pete, anyway). They definitely had their problems, but you could tell that they really did love each other, even if they weren't good at showing it. Having Jackie and the parallel Pete end up together was nice in terms of happy endings, but we didn't really get to see much of their relationship.