At the end of the last episode of the series before the credits it says "In Memory of Dwayne McDuffie".
Also, Azmuth giving Ben the new Omnitrix to replace the Ultimatrix;
Ben: But, Azmuth, I thought I proved I was worthy.
Azmuth: As usual, you don't understand. You have proved your worth. But this inferior copy of my Omnitrix isn't worthy of you.
Azmuth: OH FOR THE LOVE OF-! Look at your wrist.
Ben: An Omnitrix?
Azmuth:The Omnitrix. An improved version I've been working on, ever since you were given the prototype six years ago.
Ben: I don't know how to thank you.
Azmuth: Keep doing the right thing.
Ben: I don't suppose you'd consider giving me the Master Control.
Azmuth: Perhaps for your 18th birthday.
Charmcaster's Heel-Face Turn and friendship with Gwen in "Where the Magic Happens". Especially when she tells the guy who wiped out her magic-using species that "you can't get rid of all of us", referring to her people. And as she says this, she smiles at Gwen and holds her hand, showing that she's accepted her one-time enemy as basically a sort of sister.
Ben telling Kevin that he's like the older brother that Ben never had growing up.
This, from "Andreas' Fault", after Argit manipulates the trusting Andreas into a Heroic Sacrifice:
Argit (clawing at the ground): Oh no — I lost everything! Do you know how much money I had in there?
Kevin decks him
Kevin: He trusted you. He loved you, and you used him!
Argit: You know, I just don't understand you, Kevin.
In a sick, sad sort of way, Kevin's "Can I have Quarrel back?" in Nor Iron Bars In a Cage to the prison warden was kind of heartwarming. The interaction in the flashback between Quarrel and a newly human-looking Kevin was also incredibly cute.
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.
Ben kissing Gwen on the forehead before he sacrifices himself in "Ultimate Sacrifice".