The scene in "Pre-Filer" when Danny is playing soldiers with the two kids.
The final scene of "Skin and Bone", where the team comes over to help Rebecca redecorate her apartment.
Especially the part where Web brings her a plant and tells her "welcome to Los Angeles". Should be creepy, that Web's referring to her first case, where the UnSub killed new girls in town, but it's actually quite sweet, showing that Web recognizes that Rebecca's here to stay and that she's ready to form friendships.
The group rescuing Rebecca in "Loneliest Number" and assuring her that they're here for her.
Danny crying while listening to the suicide tapes in "Loneliest Number"