This moment from "The Rebel Rescue" when Caleb thinks Blunk is dead or captured.
Caleb: (grabs one of Phobos' guards) Where is he?! What did you do to my friend?!
Blunk: (pops up seemingly out of nowhere) Caleb call Blunk friend!
Susan Vandom kissing her (pretending) Sleep Cute daughter's head after she ran away in "Ghosts of Elyon".
Cornelia and Will reconciling, with the former calling Will "one of her [Cornelia's] girls" in "The Mudslugs".
Caleb reuniting with his father in the first season episode "The Underwater Mines".
Caleb: Welcome back to the rebellion, Dad.
In the second season episode "L is for Loser", even after Mr. Huggles is transformed into an Emotion Eater that feeds off anger by Nerissa, he is still loyal to Matt, not her. Which surprises Nerissa greatly.
In the second-season episode "S is for Self", Will finally reunites with Matt, who has been possessed by the demon Shagon for several episodes. Once Matt breaks free of the demon's control with Will's help, the two share a tender kiss atop the roof of a building. Matt then re-unites with the members of his garage band.
Nigel: Matt! Sweet! Where you been?
Matt: Finding my will to rock. Speaking of which, we're doing... "The Will To Love".
Nigel: But we didn't rehearse it...
Matt: Trust me. We'll nail it.
Matt then proceeds to do just that, singing a heartfelt rendition of the song as Will, the girl he wrote it for, watches from the front row with Tears of Joy streaking down her face.
The episode right after it, "T is for Trauma", features a heartwarming moment between Hay Lin and her boyfriend Eric. Hay Lin gets a new pair of braces, contributing to her Heroic B.S.O.D. later on in the episode after she is led by Nerissa to believe that own boyfriend has rejected her because of them (in addition to believing that her grandmother has turned to the side of evil). When Eric is released from Nerissa's spell...
Eric: Hey, you! When did you get braces?
Hay Lin: I know, they're... kinda ugly? *covers up her mouth*
Eric: How could anything look ugly on you? Besides, they're only temporary. *adorably* And they're so SHINY!
Hay Lin: *squees audibly, then glomps Eric and kisses him, lightly kicking her legs for a moment*
Similar to Hay Lin's experience, a tender moment is also shared between Taranee and Nigel at the end of "K is for Knowledge":
Nigel: Sorry I got you into trouble again. Your mum sounded pretty mad.
Taranee: That's her problem. I'm sick of always being the good girl, the smart one, the perfect child.
Nigel: I don't know. The sweet thing is, that's kinda what I like about you. *returns Taranee's glasses* Glasses and all. *kiss*
Another sweet moment occurs when Cornelia finds out Caleb is alive at the end of "F is for Facades" and promptly glomps him.
Another touching W.I.T.C.H. moment appears in the episode "E is for Enemy". Will's mom, dismayed with her daughter's slipping grades, has decided to move Will and herself back to Fadden Hills, away from her four best friends. The girls use this as an excuse to have a sleepover, which helps them defeat Nerissa, who had been intruding dangerously into the girls' dreams. Their victory celebration, however, wakes up Will's mother, causing her to charge into the room. She prepares to give Will a scolding when Taranee pleads with her not to move Will away. Will's mom dismisses the girls' pleas, saying that her decision is a "family matter". Hay Lin immediately chimes in with "we are Will's family!" and the four girls form a circle around Will, hugging her tightly. Her friends promise to help her with her studies, and Will gives a passionate speech about how much she cares about her friends and how moving back to Fadden Hills isn't the answer. Will's mother decides to let Will stay in Heatherfield, and the girls happily hug again.
In the second music opening of the series, Cornelia sees a saddened Lillian, whose flower hasn't grown. Without a word, Cornelia magically grows the flower herself. Lillian immediately brightens up.
After watching "O is for Obedience," Nerissa trapping Caleb in a lightning cage during the showdown in "K is for Knowledge" becomes this (in a really weird way): since Caleb is her son, she is deliberately trying to keep him out of harm's way.
Her protectiveness of him in "Y is for Yield" counts as well. Concern of his safety is the only way the others can convince her to work together to get a message to the Guardians.
Hay Lin's reunion with her grandma at the end of the first saga in the comics.
Shinobu trying to protect Will's brother, after his abduction by her father.
The guardians talking down Hay Lin after she becomes a Ragorlang.