Derek and Angie burying the hatchet at the end of episode 1-8 of Under the Knife/Second Opinion.
Derek choosing to join Caduceus over staying at his old hospital, because even though he loses the close patient-doctor relationships that come with working at a local facility, he believes that the potential to save far more lives as part of a major medical organization outweighs the drawbacks.
Naomi hugging Alyssa at the end of Trauma Team. With everything she had gone through in the series, she deserved the happy ending she earned.
The end of Under the Knifewith Derek and Angie reading the letters from the children that they saved in the last chapter was a very sweet way to end the game.
The final scene with Derek and Angie in Under the Knife 2 during the epilogue was terribly cute.