Oh, i dunno. There was the bit where Vala sat in Daniel's lap in The Shroud (in fact, their entire scene read quasi-romantic to me), and his behavior toward her in...um...The Episode Before This One. (Yes, kind and solicitous, but the part where he touches her on the face is extremely intimate, a level of intimacy that goes beyond regular friendship.)

I think it's important to remember that they were already over halfway through the season when they found out they were cancelled. They had been working on developing Vala's relationship with the rest of the team (Cam, Sam, Teal'c) in that back half, which meant they had to back-burner the Daniel thing for the most part. But it was still there.