Jane and Lisbon slow dancing in "Rose-Colored Glasses"
Lisbon: I used to love this song.
Jane: Love the song.
Lisbon: I love this song.
Jane: You clearly want to dance.
Lisbon: Dance? With you?
Jane: Oh, come on. You can pretend I was that mean, cold-hearted boy you worshipped from afar but never spoke to.
Lisbon: (hesitant) Well...no funny business.
Lisbon: (smiling) Yep.
Jane: (smiles, surprised)
And then they dance.
This is heartwarming as well as shipper-iffic because they are both so shy and sweet about it. You don't really need ship them to love this moment, because it reminds you that even though they don't have many other people in their lives, they have each other.
Rigsby and Van Pelt finally getting together is awesome, but Rigsby's speech beforehand is so incredibly sweet. "I don't care about the CBI. I don't care about the rules. I love you. Unless you stop me, I'm going to kiss you now."
"Lisbon, I want you to know that you can trust me. No matter what happens, I will be there for you. I need you to know that."
"If I were dying, I would want to call you." D'aww. (Also, how sad is that? She is, quite literally, the only person he has in the world).
Jane claiming that he will always save Lisbon, which is particularly sweet in its sheer ridiculousness - Lisbon is always the one doing the ass-kicking in that relationship.
When Lisbon is on the verge of tears, Jane calms her into a trance and just holds her and strokes her hair. Can y'all say Ship Tease?Aww.
The whole episode "His Red Right Hand". It's very tear jerk-y as Bosco and his team are gunned down by an associate of Red John's. Bosco has a Dying Declaration of Love with Lisbon which she seemingly reciprocates. The team then all share a drink and Rigsby starts absent-mindedly singing Amazing Grace to which the whole team join in with. Even Cho.
When Rigsby and Van Pelt's relationship is found out, they either have to break it off, or one of them has to transfer. He goes to Cho for advice.
Cho: Which do you love more, your job or Van Pelt?
Rigsby: It's not that simple!
Cho: Yes it is. Which do you love more?
And Rigsby chooses to transfer so he can stay with Van Pelt. Except she chooses to break it off, because she doesn't want him to ruin his career over her.
After interviewing some recovering war veterans, Jane thanks them for their co-operation before giving more heartfelt thanks for their service overseas.
Later in the same episode, he teaches one suffering from short-term memory loss and nightmares a few of his mind techniques. It's a side of Jane we don't see very often.
When Rigsby and Van Pelt go undercover as a couple into a radio program that helps couples to repair their relationship, Van Pelt tells Rigsby that one of the reasons she broke with him was because she felt they were not ready, but that now both of them have grown and that she likes him now. Rigsby reveals to Van Pelt that he still loves her, even after he had a son and she got engaged to O'Laughlin. At the end of the episode, Van Pelt goes to Rigsby's apartment and kisses him, entering his apartment with him.
In "Red John," Cho, Rigsby and Van Pelt all appear to distract/threaten the FBI long enough for Jane to get away, even though they are no longer CBI agents and will get in serious trouble. Jane's "Thanks, guys!" as he takes off is shouted with nearly childlike glee.
Jane writing letters to Lisbon after the events of "Red John". If you look closely at the one he's writing in the episode, he apologises to her for leaving her on the beach in "Fire and Brimstone".