You are right abou the quirks there.  My favorite to see develop has been every time they reach the scene of a risky situation Beckett tells Castle to stay in the car.  In episode one she was angry and handcuffed him in, at each episode the dialogue has lightened.  One episode he says to her, Yeah we know how that worked out last time!  Then after the ball she calmly says, "As a friend I am asking you to stay in the car", and in that episode he did really try to stay in the car and it was a funny scene with him telling the criminal "She told me to stay in the car."  I think this is just capturing how people and relationship really do evolve and how people would really bring back up past occurrences in the conversations.  This recalling of events from earlier episodes in character conversations, I think it gives the faithful viewer a tip of their hat.  I enjoy the writing and the banter–it is very real and very true to each characters personality.  The quirks are what adds for me an extra layer of enjoyment.

Aicha said:

About the coffee, I love the one scene (Can't remember which episode because I just watched a bunch of them out of order) where Castle sits down beside her and puts his coffee down, and she picks up the mug in the middle of the conversation and takes a drink. He's watching as she does it and is about to say something, then just lets it pass. I love that subtle movement while they're talking, it just adds extra layers to their evolving relationship.

I  also sit and watch several episodes at a time on my computer, and I love that scene, too, Aicha! Beckett just smiles as she takes his coffee cup, and she keeps the cup instead of putting it back on his saucer.  And right, Castle watches and doesn't say anything, but sighs af if missing his coffee.  How cuter if they both sipped out of the same cup!