The scene near the end after Doris is defeated and Lewis asks Goob to join the Robinsons. The look on Goob's face as he walks away is so sad.
Not to mention Goob's reaction when he learns that Doris was using him the whole time. "I thought Doris was my friend..."Awwww.
One punctuation mark: "?" Bowler Hat Guy has finally given up his schemes for revenge...and he doesn't know what else to do with his life.
When Lewis finally gets to see his mother.
"Mr. Steak, you're my only friend."
That moment when Lewis's hat comes off and the Robinsons realize that they can't keep him. They also can't tell him why. So Lewis gets rejected by the first people who have accepted him without question and he doesn't understand why.
Wilbur blurting out to his mother that he never planned to take Lewis back to find his mom, right in front of him no less. The opening music during that part is so heartbreaking that it makes one want to give Lewis a hug when he hides behind a topiary and begins crying.
Particularly poignant is the part where Lewis says "You lied to me?" It could be described as a hiss almost but instead of making him sound angry, he sounds legitimately and truly hurt at being used by someone he obviously had come to consider a friend and the fact that this comes after the "Guess we make a pretty good team."/"Yeah...guess we do..." exchange makes it hurt worse. Anyone who has ever felt used (legitimately or otherwise) by someone they considered a friend can totally relate.
Wilbur fading from existence because of Doris tampering with the past.
Also the scene early on when Lewis is angrily explaining to Mildred why he's a lost cause: he's already failed 124 adoption interviews (and was keeping track) due to prospective couples being put off by his zealous enthusiasm for science. To make matters worse, he's almost thirteen, and he knows it's near impossible for teenagers to get adopted. At this point, he's given up on finding a new family and has resigned to just aging out of the system alone.
Mildred's reaction to finding out he's been keeping track. She goes from telling him that he's obviously exaggerating in a playfully affectionate tone to trailing off in a deeply sorrowful voice when he shows her his tally.
Lewis' snarl of "No one wants me! My own mother didn't even want me." It really makes you want to hug the poor kid.