Pretty much anytime Reinrassic III and Ben interact, knowing how much the latter has caused the former's character to develop from a racist supremicist to one of Ben's closer friends and staunchest allies. Added "D'awwww" points for Reinny's unintentional pet name for Ben: "BenbenTennyson."
Kevin embracing Gwen after she frees him from the horror of a transformation into kadanite.
Gwen assuring Ben that she knows Julie would be thrilled to go out with him.
Gwen holding Ben in her arms when he nearly passes out in "Darkstar Rising."
Ben in "Alone Together". Pretty much everything he did.
The entire ending of "Voided". Period. To be more specific, not only does Ben save the world, but also he and Gwen find that Grandpa Max is still alive. Then, while Gwen is trying to get Ben back through the portal she opened, Kevin reaches in to help her and utters the following line:
It's time to come home, Ben.
The last five minutes of "Paradox", where Paradox takes his assistant on a trip through time. Said assistant has been an outside-of-time force for a while and has just been brought down to an old man.
At the end of Eunice's first episode, Ben sticking up for her against Azmuth when the latter wants to deactivate her as a non-necessary Omnitrix prototype. Ben was ready to fight his old mentor over that one.
The ending of "Save the Last Dance". Discounting the weirdness of Ben playing Mr. Seahorse, those Necrofriggian babies are cute. And Kevin giving Gwen the honor of a private dance, even though they didn't make it to the school dance, just adds to it all.
Papa Wolf moment of Rath in "Con of Rath". After saving the little ice cream-like prince from a stomach of a newly introduced villain, he threatens to make a sweater from his ORGANS in case he declared war with another alien race. Also qualifies as the Crowning Moment of Awesome.
"Inside Man": Ben rescuing a DNAlien rogue from being taken back to their ship, along with two words: "No sacrifices."