The scene with Danny and Sam above the clouds at the end of Facing The Future. There's even a pic of the moment.
In Trial By Fire, when Sam learns that Undergrowth captured her parents, she's absolutely ticked and wastes no time in saving them. Shows that no matter how much they drive her insane, Sam does care about her parents.
Danny and Sam confessing their love for each other at the same time in Hearts and Minds.
Danielle being adopted by the Fentons in A Family Thing. Especially this part:
That was it. In that instant, Danielle completely lost all control, grabbing onto Maddie's suit and clinging to it for all she was worth as she choked and sobbed. Even Sam couldn't help but hold Danny's hand a little tighter and rest her head on his shoulder as Danielle buried her face into the crook of Maddie's neck and began bawling uncontrollably, all of her pent up emotions and loneliness pouring out of her like a flood.
"Ssssshhhhhhh...it's okay, Honey." Maddie cooed softly in Danielle's ear, softly stroking her hair as she wept on and on. "It's okay... You don't have to worry anymore...I promise..."
"...You're home now."
And Tucker's response:
"I mean, come on. If I can't abuse my municipal authority to give a little girl a place to live, what am I even DOING in this job?"
Danielle hearing Danny call her his little sister in Stolen Years.
The entirety of What She Wants.
The scene between Little Danny and Sam before they return to normal in Stolen Years. Even Maddie and Jazz thought it was touching.
At the end of the story, there is an adorable scene between Danny and Maddie.
Every time Sam gets through to Danny when he's in his feral Super Mode.
Ancient History has one in regards to the relationship between Tucker and his secretary Tanya. Tucker has evolved to respect Tanya enough to let her keep her memories of the Hotep-Ra incident and promotes her to being campaign manager. When Tucker asks if she has any doubts he can win, Tanya's response brings a smile:
Tanya: Do you really think I would be working for a 15 year old boy if I didn't BELIEVE in him?
It's especially heartwarming when you remember earlier she called Tucker out for not revealing his experiences with Hotep-Ra and Ghost Tucker.
Any scene with Danielle and Wulf can make you smile on the darkest day.