It might be a weird entry but the Jets' apparent disdain of Shrank and Krupke's racism towards the Sharks. Sure they're rival gangs, sure they're leading violent lives that can only end in tragedy, and sure they do honestly hate the Sharks... but they refuse to let it be about racism. For them, it's something else entirely.
Tony and Maria excitedly discuss how they would get married in the sewing shop, using mannequins to represent their parents and friends.
Likewise, both gangs briefly get together to mouth off to the cops. They even stick up for one another. Oddly enough, if the cops were around more often, the gangs probably would've cooled off eventually.
The fire escape scene. The whole scene is one long CMOH.
For all their faults, Bernardo and the other Sharks do seem to genuinely love and care about Maria.
For all the tragedy, Maria not committing suicide unlike Juliet is a case of a minor moment of both heartwarming and awesome. (Some theatre versions, such as the Australian tour in 2010 (the troper saw this production) makes it clear that she is determined to live.)
This little exchange between Anybodys and Ice. It really shows that she's been accepted as one of their own.
Ice: You done good, buddy boy.
Anybodys: Thanks, Daddy-O.
And earlier, after Anybodys warns them Chino is looking to kill Tony and the Jets reveal that for all their Jerkass ways, they genuinely care about each other:
Ice: "Tony came through for us, so we gotta come through for Tony."
At the very end, as Shrank and Krupke escort Chino to the police car, Shrank can be seen putting his hand on Chino's shoulder in an almost comforting gesture. For someone who's been such a jerk throughout the movie, it's nice to see him showing a bit of compassion for this young man who's not only lost his best friend and fiancee in one day, but has also ruined his life, as his act of revenge will undoubtedly send him to prison for a long time.
The stage show has a surprisingly humanizing moment for A-Rab and Baby John, when they find each other in the streets after the rumble, when they try to console each other, A-Rab encouraging Baby John to still walk tall and not let people know how much Riff's death got to them. And then...
A-Rab: ...I wish it was yesterday. Baby John: Me too.
This is soon followed by "Gee, Officer Krupke," which in this context, comes off as the Jets trying to cheer each other up, and possibly find a bit of humor in all the tragedy just to keep themselves from going insane.