My choice for S9 is probably not that big of a surprise, given that I love pre-series/wee-chester stuff.
S9 - John shows up to collect 16 year-old Dean from Sonny's
Why I chose this scene:
Surprisingly enough, I think this was backstory that I really needed on Dean - to me, it explains just WHY Dean was so devastated by Sam leaving for Stanford. It also humanizes Dean to me, in a weird way... in that we see that Dean also had a chance to escape, like Sam did, and clearly WANTED to take it, but in the end chose not to... and chose not to not for the reason of "hunting is awesome and Dad knows best!" which is a lot of how Dean came across in the early seasons (when we were seeing him mostly from Sam's pov.) This complicates that. This chose that even before S3's revelations of Dean's resentments towards his father - Dean KNEW about them and struggled with them. I don't know if I'm articulating this correctly, so apologies if now - but to me, this really enriches an already rich character, in that it takes his internal character struggles back even further, which in turn makes them even more impactful to me. It also makes Dean's comment in Scarecrow about being PROUD of Sam for leaving, for being who he is, stand out all the more... because YES, Dean resents Sam for it, because Sam was the reason that Dean didn't leave, but Dean is also PROUD of Sam, because Sam did something Dean ultimately wished he could have done, but felt he could not. (Just, without even arguing which decision was the right decision - I don't think Dean leaving would have made him a bad person. It's that thing about affixing your own oxygen mask before helping someone else, in my opinion. Dean's tendency towards martyrdom is a debate all on its own though.)
But, this scene tells me why Sam leaving was so devastating to Dean - because Dean stayed BECAUSE of Sam. (Regardless of whether Sonny would have been successful with the petition) Dean gave up his shot at freedom and a second chance at life, because he didn't want to leave Sam behind. Of course, by nature and circumstance, it's impossible for Sam to return this gesture of devotion - because a)Sam didn't get his chance until Stanford, and b)Dean is his older brother, who was always firm in his decisions, who - more importantly - got ALONG with their father, and who didn't seem to need protecting. So, we really only see Sam return this same level of devotion when he has to save Dean from death (and we shall not speak of S8, which was a writing travesty). I also think that it's unfair for anyone (possibly Dean) to consider Sam ungrateful for Dean's decision, because a)Sam never asked him to make it, and b)I think Sam WAS grateful that he had Dean, but Sam didn't realize that Dean needed him when they were traveling with their dad just as much as Sam needed Dean. We see a similar thing happen with Dean at the end of S2, when it's only when Sam bluntly ASKS him "what do you think my job is?" that Dean realizes that, at least n the absence of their father, Sam considers it his job to protect Dean as well.
ANYWAY, this is all a really long winded way to say that I love the character exploration that occurs in this mostly silent scene. I think the actor, whose name I momentarily forget, did an amazing job with Dean as well. I know some people disagree, but I think definitely acting-wise, he's the best young!Dean we've had. Just the way he plays this highly emotional scene, is so reminiscent of scenes we've seen Jensen do...like Heaven and Hell, and just that..."I want to cry, but I'm not going to cry, but I'm crying, but I just won't mention it and no one else mention it either please" and yeah.
The final thing I love about this scene is the ways you can read it. Like, the fact that we see everything from Dean's POV, so - is Sam seemingly acting too young for his age? Well, I think that's frankly how Dean sees him. I know, originally, they were going to play this episode as Dean being 14 and Sam being 10, and then they aged Dean up to 16, making Sam supposedly 12. But I love that we can also use this kind of clumsy script change as an amazing work of unreliable-narrator... because I remember when my little sister was a young teen (we're six years apart), and whenever she wasn't directly infront of me, I would still remember her as a child. And, while it's not related to this scene in particular, I love how we can contrast Dean in this episode (at 16) to Dean in After School Special (at 18) and the VAST DIFFERENCE, and then realize that After School Special was told from Sam's POV, and of course Dean would be this adult-looking Lothario of a guy. But that's all off topic.
I also love Sonny in this scene, because he's a good dude, and he's the kind of person that Dean needed more of in his life.
ETA: Oh man, I also forgot that this is the SAME YEAR that Dean "embraced the life" according to what he told Gordon in S2 - which to me makes perfect sense. Because if you make a decision to be trapped somewhere, you're going to change the story to be one where you PREFER to be there, rather than a story where you wish you could have left. You rationalize it to be something you want, so that you don't have to admit to being miserable. We do it all the time. So, this scene just completely fills out that story too. It could have very well been the hunt directly after this... Sam waiting in the car, Dean and John killing a werewolf, and Dean is like "yeah, what other kids get to kill werewolves, really, I should find this awesome, and ignore the fact that we live out of abandoned shacks and cheap motels, and I've been practically a single-parent to my little brother since I was at most 8 years old."
There's probably much more I want to say about this, but it's nearly dinner time and I'm getting hungry and it's hard to think. So, discuss with me more in comments if you feel the urge!