"Beyond Belief", and Cal using semicolons as a way to both apologize to Emily and to give her new boyfriend a chance to prove himself.
The final scene in "The Canary's Song": "Thank you for cleaning up my mess, Gillian."
Loker to Foster, after lying to protect her despite his "Radical Honesty" policy: "You have to have faith in something. I'm putting mine in you."
Lightman's surveillance of the men in Foster's life, while a little invasive is also a testament to just how important she is to him.
Foster: You thought Alec was having an affair, didn't you? That's why you followed him.
Lightman: ...I was afraid you were going to get hurt.
Foster and Lightman in the hospital after Foster is attacked in "Blinded". The way they just keep looking at each other, and keeping physical contact, as if they're both scared the other is going to disappear, is a hybrid of this and Tear Jerker.