This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Short Circuit
It's a minor thing but, the squashing of the grasshopper. Poor Johnny didn't mean to do it. And the resulting talk about death with Stephanie is when it suddenly dawns on him that when NOVA show up, they're basically going to kill him.
Johnny Five: Squash... dead. Disassemble... dead. Disassemble,DEAD?!'[immediately flees in terror]NO DISASSEMBLE!!
Johnny Five's apparent demise in the first film. Yes, it's a Disney Death, but still... Even Howard seemed pretty despondent, (and not just for losing tech worth millions of taxpayer dollars) just before firing Skroeder.
During another reading binge at a bookstore, Johnny finds two books that he says he will read "very carefully". After he is arrested by the police, and treated as property rather than a person, he's shown reading one of the books slowly and carefully, rather than flipping through in seconds like he normally does. The two books? Frankenstein and Pinocchio, both about man-made creations who were brought to life, just like Johnny himself.
Johnny's understandably hurt reaction to learning Fred was going to sell him out (literally).
Johnny: Fred wants to sell ME?'! Fred: (laughs sheepishly) Oh, J-5, c'mon, it's just a figure of speech. Johnny: Am not property, Frederick! One whose person is under control of another as master, is a SLAVE!
The look on Fred's face when he finally finds Johnny... and sees the condition he's in. His expression goes from joy to horror in seconds.
Johnny getting Fred's name wrong may seem funny, until you remember some of his brain is still damaged.
Fred: Are you okay? Johnny Five: Functioning 100%. Perfectly ko Derf. Fred: It's Fred. Johnny Five: That's what I said, Derf.
The aftermath of Johnny Five's beating by the bank robbers. Also, near the end, when Benjamin tries to revive Johnny Five's battery power with a defibrillator, just after catching Oscar.
Crosses over into Crowning Moment of Funny, but after Ben revives, Johnny, he threatens the paramedic who loaned him the defibrillator:
Ben: Keep that power on or I'll beat the living headlights out of you!
It is equal parts this and Nightmare Fuel, but during the beatdown he gets from the bank robbers, Johnny is screaming in pain and pleading for his life while Oscar continuously yells to the robbers to smash Johnny. One of the robbers (who was shown earlier to be a tech genius and borderline Minion with an F in Evil) hesitates for a second before committing himself to help in the smashing.