And when he actually comes back to say goodbye to Shawn as a ghost, and later, during the finale, turns on the radio, but being a ghost, he's just a quiet observer commenting on how much Shawn has grown and leaving him to things down on Earth while he goes back to Heaven.
After Topanga moves away, at the end of the episode Cory's still standing in the backyard, watching the road to see if Topanga's car turns back (it never does). Eric walks into the scene a minute after, and tries his best to console Cory - but in the end, even he knows there's nothing he, as his big brother, can do to make him feel better about the situation. Wham. And then Cory asks him if he could keep him company while he continues to watch the road, and of course, he does. Double wham. Verge of tears, man.
"I'll be your father." Cue waterworks.
"Resurrection" and "Can I Help to Cheer You?" are heartbreaking due to the sheer amount of hell they put Eric through.
Eric: I can't be your dad, Tommy.
Tommy: Why not?
Eric: (sits Tommy on his lap) These people in California, they sound really... nice.
Tommy: But I want to be here with you!
Eric: You're gonna have a house with a mom, and a dad, and a big pool, and a big sister, and a dog named "Waldo."
Tommy: I don need a dog, I have you! Eric I'm never going with anybody except you!
Eric: I'm not going to adopt you Tommy.
Tommy: Why not?
Eric: Because... I'm not.
Tommy: (pleading) Yes you are!
Eric: Tommy... I'm not going to adopt you.
Tommy: ...I don't like you anymore.
Eric: I'm sorry to hear that Tom...
Tommy: And I'm going to California to be with people who care about me.
Eric: Good for you Tommy. Good for you, man. (Eric leaves the room, closes the door, and starts sobbing)
Orphanage Official: (to Eric) Good for you.
The Flash Forward in "Seven the Hard Way", showing what would happen if the core group didn't settle the argument which was on the verge of ending their friendships - Cory & Topanga are having marriage counselling, Jack's become just like his stepfather, Rachel wound up marrying the boyfriend who she broke up prior to her first appearance, Angela & Shawn have fallen apart but still love one another, Shawn doesn't speak with Cory or Topanga anymore, and no-one's heard from Eric in years. The scene then undergoes a Mood Whiplash when Eric turns up... having become a hermit, married a moose & changed his name to "Plays With Squirrels", only for the scene to undergo anotherMood Whiplash when Eric gets Jack to read his several thousand page manifesto, which only features one thing written on the first page.
Jack (Reading Eric's manifesto): Lose one friend, lose all friends, lose yourself.
Shawn: So why are all the other pages blank?
Plays With Squirrels: Nothing else seemed important.
The end of Cory's storyline in "The Psychotic Episode". Cory's afraid of everything changing after he gets married and that's what's been causing his nightmares.
The scene with Turner at the end of "Cult Fiction." Shawn's monologue/prayer while Turner sleeps is great, but the moment before with Cory is just as great and less-often mentioned.
Cory: Shawn, this is a hug. Okay? This is a hug! And this is when you hug somebody. When you care about them and you want them to know that! Now, you cannot leave here, do you hear me? Turner took care of you; he loves you. And you love him. Is that real? Or are Mr. Mack and the Center real? You decide. But you cannot go. We can go. (Cory and Topanga leave)
The fact that Minkus left after the first season qualified. Think about it: all of the other characters got some development beyond their stereotypes, but he just was remembered as "the nerd". Think of where the series could have gone if he hadn't disappeared. It appears that the spinoff might change that up a little, as his Expy (and son) Farkle will likely be sticking around for season 2.
Shawn brings a lot of these to the series in general. His entire speech to the sickly baby Joshua in "Resurrection" doubles as this and a Crowning Moment of Heartwarming.
"All you had to say was no." Fortunately, Alan had a very good reason for refusing to allow Cory and Topanga to stay with them.
The culmination of Shawn's and Angela's relationship following a stumble that makes Angela fear that she'll just hurt Shawn by trying to get back together. The entire two-parter is just a series of Tear Jerkers as Angela finally gets to be with her father, Angela decides to go to Europe for a year, Shawn attempts to impress Angela's father by joining the army (even though it's the ONE THING Angela is against because it created so much space between her and her father), and finally Angela's father getting Angela to admit to Shawn that she is and forever will be in love with him. Pass the Kleenex please.