Adrian's brother Ambrose confessing to Adrian that the reason he never went to see him after Trudy died was that he felt guilty because he asked her to get him cough medicine when her car blew up. Ambrose breaks down crying "It was me Adrian! It was my fault!" and Adrian hugs him assuring it wasn't.
The entire episode with the dogs.
The episode where Monk finds the man who killed Trudy. It's revealed that he's in the hospital, grievously injured. Monk steps in to talk to him about Trudy. He openly talks about how much Trudy meant to him and how he'll never love a woman the same way again. As a demonstration of how much she meant to him, Monk turns off the morphine drip, relishing the pain the killer feels, describing that as the thing he himself wants to do. Monk then turns on the morphine drip, stating that, that was what Trudy wanted. A very powerful scene showing us a visceral scene of just how much Monk was devastated by Trudy's death.
Monk: "This is me, turning off your morphine... And this is Trudy, turning it back on."