Well, I'm a big fan of Doctor/Rose, so I see little hints about them.
Like how sensitive the Doctor is in general when a new companion asks him about Rose. Like before, Martha got really put down when he kept talking about her, in The Shakespeare Code, when they are laid on the bed, the Doctor talks about Rose loads and Martha gets upset because she loves the Doctor too, and they are sharing a bed so she's gotten her hopes up. o.e
One that I saw recently was how Amy recognised what the Doctor and River might be to each other. Amy said something along the lines of "You fight like an old married couple" and I swear I remember River saying something like "Well, not yet."