Sam figuring out that the Most Holy Man could be a saint
And finding saintly body parts online
Dean and his cold pizza
Margaret Astor flirting with Sam
Sam flirting back
Dean being pretty disgusted with the flirting
Lovely closeups in the flirting scene
Sam and Dean Bond
'This isn't a perfect world we're trying to save, okay, and if I'm not perfect trying to save it, so be it'
Beautiful lighting in the scene outside Greenstreet's house
Dean flirting with the girl in the coffee shop
The way this girl is perfect for him, as an Asian beauty who's into the supernatural
Sam cock-blocking him
Sam figuring out the Malta connection
'Look at you, you're like a Boy Scout '
'You're like a... I don't know what you're like'
Dean saying 'whack'
Dean angrily handing his keys to the mob goon
The way Dean is so unafraid and snarky with the mob goons, and Sam is always trying to keep him in line
Sam being an annoyed little brother and bitching about Dean 'feeling it'
Dean figuring out how to easily clear the hotel
Dean going into a panic when he sees Sam on the floor, and checking for a pulse
Dean being concerned about Sam's head injury
And touching Sam's Disney Princess hair
And Sam not liking his hair to be touched
Sam being so angry at Father Lucca, and then coming over to his side
Father Lucca himself
Father Lucca's speech about the world not being perfect
Dean talking about what he'd do to anyone who stole the Impala
And the look on his face and the way he's not listening to Sam at all
'Oh look, it's your girlfriend'
Dean and Lucca in the car, talking about good things and God things
'What are you doing?' 'Creating a distraction'
Not a Cop calling Sam 'Lurch'
Greenstreet turning the tables on Astor
'We all have faith in something, even it's just a hunk of bone'
The guys realizing Father Lucca is a Most Holy Man
The talk afterward in the bunker
Particularly the way Sam was a little desperate and teary-eyed
Particularly the way Dean bit his lip and said he had faith
Nobody else did what Sam would normally do
When the brothers split up, Sam wasn't left out of the story
No Colonel Asmodeus
Basically, no ensemble cast taking up what should be Winchester Time
Something else that I'll discuss in the comments