Beckett: When I'm not here, do you guys braid each other's hair and discuss who's your favourite Jonas brother?
Esposito: No... but it's Nick.
Ryan: Absolutely Nick.
Esposito throwing Ryan up against a wall in "Knockout", after finding out that Captain Montgomery was involved in Johanna Beckett's murder. And the heads of a thousand Slash Ficwriters exploded...
It gets better in "Dance With Death", when a (keep in mind, married for seven episodes) Ryan pretty much insists Esposito wear his wedding ring when interviewing suspects at a strip club... to see if strippers will flirt with him even if he's not taken. The scene is set up to look like a proposal, which isn't even mentioning the subtext that Espo gets a date because of the ring... and later, can't take it off because his finger's too big and needs Beckett's hand cream. Ryan panicked. Slashers squealed.
The best thing about the Ho Yay here is that Esposito and Ryan pretty much acknowledge the fact that it's there and just roll with it.
Between Castle and his old high school friend Damian in "The Last Nail." Teenage boy sent off to a boarding school, gets homesick, and gets comforted by an older student.
In "Probable Cause", Esposito assures Beckett that she's not alone in worrying over Castle's situation as the prime suspect of their current murder investigation.
Esposito: I know how you feel about the guy. I love him, too.
In seasons 6's episode "A Murder is Forever", the victim of a week is a renown relationship therapist with a best-seller on relationships, and after having read it Ryan refers to it... but in the context of his relationship with Esposito, not his wife.
In "Under Fire", with Ryan and Esposito trapped in a burning building and Ryan's wife going into labor, they manage to contact the crew, and Jenny asks her husband what to name the baby. His response for a boy's name is "Javier". Even Espo criticizes that choice. Luckily for both of them it's a girl.
In the Season 4 blooper reel, Adam Baldwin grabs Nathan Fillion's butt. He responds by swatting his hand away and saying, "Later."
Several seconds later, the two (almost) kiss.
The killer in "The Mistress Always Spanks Twice" is the victim's female roommate, whose Motive Rant for killing is loaded with Les Yay with a Psycho Lesbian twist. Add in the fact that the victim once compared her to a dominatrix...
The female plastic surgeon in "Disciple" is absolutely fascinated by Beckett's "perfect face" and takes every opportunity to invite Beckett to come in and have some work done. Gets far, far creepier once it turns out it is extremely probable she was the real mastermind behind the killings and picked up all of 3XK's methods by dint of being his lover.
In the eighth season, Hayley and Alexis are drinking scotch in the PI office on a stormy night, wearing very nice dresses (at the same time Castle and Beckett are having a date night at home).
Hayley: Looks like we're going to be late. Frankly, I'm in no mood to leave this party thanks to your father's excellent taste in scotch and daughters.