When Ed and Eddy fake their own death via quicksand while Edd watches and breaks down. Eddy and Edd have a fight about it and Edd walks out, saying that he would rather get his ass kicked by the kids than to wander off with "a so called friend." When Eddy sees that Edd is serious about leaving, he breaks down and cries, admitting that everything was his fault. Edd is so moved by his apology that he decides to come back.
The part of this scene where Edd states that Ed and Eddy are the only two people he cares about, especially when he considers how distant his parents are made out to be in-universe. The fact that he's given up on his parents ever being there for him makes the eyes water.
Also, when Edd decided to leave Eddy, Ed's words are also tear jerking:
Ed: Say it ain't so! We are three no more, Eddy! Like hop, skip, and no jump! Like up, up and no away! Like blah, blah without the other blah!
Really though, the delivery of Eddy's line is the real clincher:
Even though it was obvious Ed and Eddy were in no real danger, just watching Double D's reaction to watching his friends drown in the quicksand, and completely breaking down when he believes that his only two friends are dead.
Everyone watching in utter horror as Eddy is brutally beaten up by his older brother and the revelation this is how he's always treated him.
The moment is even more heart wrenching when we remember just how much Kevin hated Eddy and feared Eddy's brother, and now he's sticking up to his fear on the behalf of his mortal enemy.
After spending the whole movie chasing after them for going too far, this is the moment they realize that when having to put up with a brother like that, is it any wonder Eddy turned out the way he did and end up causing all their misery to begin with?
The reason why Eddy is such a selfish jackass. He wanted to be liked by everyone by making up stuff about his brother and hiding his true, vicious nature.
Eddy: I made it all up, Double-D. Everything about my brother was a lie. I just made things up, so everyone would like me, think I was cool. But boy was I wrong. The scam, my brother... when am I gonna learn, Double-D?
Just seeing what an Extreme Doormat Eddy becomes when his brother abuses him. The most confident, headstrong of the Eds can only whimper and brokenly smile as he begs his brother to stop. And this movie reveals that this abuse had been going on this kid's entire life.
Edd writing the letter at the beginning. It's much quieter than most scenes in the show.
As he starts trying to describe exactly what happened, Edd suddenly starts using adjectives such as "immoral," "thoughtless," and "hurtful," getting angrier at each word. This could be showing how unbelievably guilty Edd feels about the whole thing...or it might be Edd finally losing his temper with his barely-there parents.
Even more is what he says upon writing the letter: "GAH, WHAT HAVE WE DONE!?"
The moment is mostly downplayed by showing how the kids now consider the Eds to be their friends, but the kids beating up Jonny for attacking the Eds can still count. Jonny thought they still wanted revenge on the Eds so he showed up and tried to be a hero again, but instead he made himself the villain and got beat up for his troubles. If he had arrived five minutes sooner he would have been part of the big group of friends celebrating in the end.
What makes this even more depressing is the fact that out of all the neighborhood kids, Jonny hung out with the Eds the most, being the closest to them in terms of association. In addition, he was also considered the outcast, what with him befriending a piece of wood, and now that the Eds have finally been accepted, Jonny is now considered the only outcast, along with his wooden companion Plank. His Sanity Slippage after the end credits just adds on to the depression, especially when you consider the reason Eddy, along with his two friends, themselves became outcasts.
A pretty big meta-example. Ed Edd n Eddy ran for 10 years. 10 long years, and now that the movie's final moment has rolled, it's over. Such a great cartoon had such a great and dignified ending, which is more than a lot of shows can say, but in the end, it's sad to see that all the adventures with that group of kids we've come to know and love is finally over.