When they're sitting in the pub going over case notes and discussing how to deal with the annoying Yorkshire policemen working with them, and they plot to make them dig up the entire farm as revenge. It's the first moment we see them truly getting along, and though it doesn't last, it foreshadows just what their relationship will become.
When Barbara tactfully rescues Lynley from an awkward encounter with his Unrequited Love and her husband.
Lynley comforting Barbara at the end of the case when she confesses what happened to her little brother, telling her "You're not a monster," and handing her his handkerchief.
Lynley has earlier damaged his friendship with his best friend, a teacher at the school, after having to officially ask him on the record about his sexual orientation, forcing his friend to come out of the closet. From that time on, his friend has been addressing him coldly as Inspector. Their last scene together:
"I'm so sorry. Can you ever forgive me?"
"If — when I can, Tommy, I'll send you a postcard."
Also, just before this, Lynley and Havers are about to interrogate a schoolboy who's at the heart of the case. Lynley tells his friend that by law, an appropriate adult must be present, and he can't think of any adult more appropriate than his friend.
Havers has been harbouring a feeling of Et Tu, Brute? towards Lynley for a while. Then:
Havers: Webberley wants a coverup, and he's relying on your loyalty to him to get it.
Lynley: No, see, that's the thing I think you've got wrong. I think he's counting on my loyalty to you.
Havers: To me?
Lynley: [nods, smiles]
And then immediately after:
Lynley: You are not meant to know this. Weberly wanted to have you sacked. I had to persuade him to let you stay. Which is why I wasn't going to let you throw it all away. [hands her her resignation letter]
Lynley: All I'm saying is, if you're leaving - if you're really leaving - I'm going to miss you.
This is capped off by the final moments of the episode, with the two of them standing next to a bonfire. After they've finished burning what they came there to burn, he turns to go - and she stills him by placing a hand on his chest, then throws her resignation letter into the fire. No words are exchanged. They don't need to be. From that moment on, their trust in each other is absolute.
Barbara is held hostage at gunpoint - on her first case back after taking a bullet to the stomach in the series 3 finale. She's terrified out of her skin, but largely keeps in control until she is rescued - at which point she whales the tar out of the hostage-taker until Lynley pulls her off, then bursts into tears and cries herself out against Lynley's chest as he holds her. The kicker? He kisses the top of her hair as she cries. The scene, in full, is here.
Lynley shows up at Barbara's flat in the middle of the night. Heartfelt and emotional baring of souls ensues, concluding with the mutual admission that they are each other's reason to get up in the morning.
Havers is struck down by the villain with a stone to the head. Lynley forgets about chasing the villain, runs up to where Havers is lying on the ground, lies down besides her, and brushes away a few twigs from her hair to make sure that she is all right.
Nathaniel Parker saying, after the show ended, that the worst part about leaving Lynley behind was not working five months of the year with Sharon any more. When he did a guest spot on Lewis, another crime drama, he noted that he kept looking around for her and being puzzled when she wasn't there.