Awwwwwww... - when the Commander's two young children ask to sleep in his bed after they have nightmares and slowly take up all of the room. He retreats to their bed and they follow him after they have nightmares, eventually falling asleep on top of him.
A lot of the Commander's other interactions with his kids are pretty adorable also.
Not a test, where the Commander buys Jared a sack full of Beanie Babies for Christmas, as it's his first Christmas away from home. Jared worries if it's some kind of test and it isn't.
Jared hugging the Commander afterward is half this trope and half Crowning Moment of Funny.
The Commander's response to Jared "outing" Poison in general — he seems baffled at the idea that her birth gender assignment might bother him at all.
Commander and Canada having a beer together after the "Gackt" arc.
Pretty much the entire panel.
The Commander empties the Epic Jar. What's more, he says that the other manly guys were in on it as well, showing that they also like and appreciate having Jared around.
Awwww, the Commander really does care, and is trying to be a parental figure for Jared (who suffers from Parental Abandonment).
While small in comparison to the other things the Commander has said, saying that he will still defend Chuck Norris' nondescript spacefuture freedom to say whatever he wants (including that said nondescript spacefuture has a stupid religion) is still heartwarming.
This moment◊, where the Commander (realising that Jared is useless as a fighter) tries to make him a part of the team (as the potion holder), is oddly heartwarming on The Commander's part.