The car scene for me too, last season, just before he leaves SB. He tells her he wants her to be happy.
I like the scene in Neverland on the ship, after they rescue Henry, he tells her she raised Henry well. I think he is the only one onscreen to give her some credit for that despite Regina and Henry's rocky period in s1.
I also liked the scene on s2 where Regina is mourning Cora and he comes to pay his respects. Tells her black was always her color and tries to advise her to give up her quest for revenge against Snow so she does not loose Henry.
There are actually alot more scenes I like from s 1+2. Hard to pick just 1.