When, after getting to know the real Sector Z, they reverted back into their Delightful form.
"Tell the Kids Next Door we miss them!"
Or later on, when we see Numbuh Zero once again as Numbuh One's bumbling dad, with no memories of being a KND operative. "Just playing with an old friend, Dad."
Numbuh Zero's final message to Numbuh One via the broken recommissioning module at the end of Operation Z.E.R.O. is both heartfelt and heartbreaking, saying that while he might not remember what he did, he wants to go on his greatest mission: being a father to his son.
In earlier episodes, the whole process of decommissioning is glossed over. Then in the opening of "Operation: M.A.U.R.I.C.E.", we're introduced to an operative, Numbuh Nine, who's a good friend of Sector V. It's his thirteenth birthday and he's willingly going to be decommissioned. The combination of his speech, his screams while getting his memories wiped and walking out as a sullen teenager with no memories is pretty damn depressing even if it was all an act. And the Crowning Music of Sadness makes things even more emotional.
Decommisioning itself is a gloomy process. Imagine losing most of your memories from your childhood. Imagine forgetting your crushes and your best friends, and acting like they never existed.
Numbuh Two: Who was that guy? Numbuh One: ... A comrade.
The ending of "Operation: I.N.T.E.R.V.I.E.W.S.? Adding extra weight to it? It's the audience's goodbye as well. It's been a great six season run, and seeing it come to an end is just heartbreaking.
Numbuh One: Just promise me one thing, that you'll never grow up, not even if you live to be a hundred and don't have any memories of our adventures together, you'll still be a kid at heart.
"Operation: F.O.U.N.T.A.I.N.". It's pretty sad when they begin to contemplate what will happen to Leona when 300 years of suppressed aging will catch up to her. Even after they save her, and she double crosses them, and they save her again, as 1-4 year olds. Waving goodbye to her fountain, watching it crumble to the ground. Her finding a different one and laughing made up for it, a little.
Baby!Numbah Four: I thought we came here to save Weona.
Baby!Numbah Five: Change of plans! She's an adult and a jerk!
Also that near the end it seemed Leona was going to pass away from old age
"Operation: S.L.U.M.B.E.R.", where Numbuh 86 has to invent a super-secret, girls-only mission to get people to come to her slumber party.
Numbuh 86: I know it's unusual, but my mom is forcing me to throw a slumber party and... I had to invite someone. Numbuh Three: Why didn't you invite some of your own friends? (Numbuh 86 hangs her head) Numbuh Three: Oh.
It makes the moment at the end, where Numbuh Three insists that she's 86's friend, all the more heartwarming.
Lizzie's breakup with Nigel is unexpectedly serious. She recognizes that Nigel's duty to the Kids Next Door will never give her the boyfriend she wants and decides that breaking it off would be for the best. Might not drive someone to tears but it is a well-handled moment of drama that can inspire some empathy from the viewer.
Numbuh Four is having fun in his time as a "bully fighter", playing matador to caffeinated adults who act like bulls. The heavy stuff comes when at the championship, his next adult to fight is his father (whose face is shown for the first time).
Also when he learns the dark side to the fights: adults are lured, captured and thrown into pens and force-fed enough caffeine to make them charge at anything, even their own kids. Numbuh Four's Dad got roped into the whole mess because he believed he was going to a seminar... on being a better dad. OUCH.
The last image◊ from the series is enough to make anyone bawl.
In Operation C.A.R.A.M.E.L we learn why Heinrich holds ill will towards Numbuh 5. 5 years, 5 months, and 5 days earlier an incident happened that gave Heinrich delicious caramel unknowingly at the cost of what he valued most. Turns out he used to be a female and she had lost what she had valued most, her beauty. Assuming Heinrich is 10 like Numbuh 5, this means Heinrich lost what he had valued most when he was only 5. At such a young age losing something that important to you would do severe psychological damage.