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.
The Commander's daughter wants a millipede. The Commander hates Millipedes, so he gives her a list of things to do before he'll give her the millipede, namely a bunch of research on how to care for them and several months of a boring tedious task. She follows through, so he gets her the millipede. Jonesy asks why he didn't just pull the Dad Card and say no, since he hates millipedes:
Commander: Well just 'cause I hate millipedes doesn't mean she should haff'ta.
In addition, there is some Fridge Heartwarming during the moment where he learns Hyper Beam. Mr. Fish is shown to be capable of choosing which move to replace Hyper Beam with. One of the moves shown is "Don't Eat Jared." Jared is arguably the one thing that is stopping Mr. Fish from being completely free (as he's still technically a wild Pokémon), and Mr. Fish outright avoids deleting that move. This shows that Mr. Fish does genuinely care about Jared and wants to avoid harming him if at all possible.
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.
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.
Despite being the cause of the EldritchApocalypse, the Commander proudly acknowledge Jared and Jonesy anyways. The former for leading his men in his absence and showing he has a real presence over them, while the latter for being great towards his friends and family in the future and treating them as regular people. And admitting he was at fault as well.
Commander: Pretty good day all things considered, I'm proud'f us.
Another Commander-Jared moment, when Jared expresses a desire to get fit, The Commander acts as his personal trainer, giving encouragement like telling him he can be athletic without being a 300-pound musclebound hulk, to worry about his progress and not what others are doing, and in general building his self-confidence to get him past that initial wall.
As mentioned several times above, the Commander's relationship with Jared. It's clear through many of their interactions that the Commander is a more loving parental figure than his own parents, giving him fatherly advice and at one point comforting him after a hurtful phone call from his real father. What's more, his kids obviously adore Jared, and their interactions together are very much like that of an older brother playing with his much younger siblings. Even if his real family treats him like crap, Jared's loved and welcomed in the Lobster household.
Jared seems to be taking some of Commander's philosophy that "manliness" isn't defined by being a musclebound tough guy to heart as well. He's a bit less obsessed with becoming physically strong like the other guys at the office, and he even openly gushes to Commander about things that would likely get him laughed at if Commander were the stereotypical "manly guy". When he shows Commander and Jones that he learned how to crochet Yoshis while they were at the Survival Dome, you can practically feel his pride.
June: Jared! Jared! Can we ride Mr. Fish? Jared! Huh, Jared?
Jared: *cheerfully* What's the magic word?
Jared: I'll take it! *cut to the three riding Mr. Fish in obvious glee*
Double points for being the only word Sam has spoken on panel in the whole comic.
The reveal that Commander Badass is, to his team of time-space marines, effectively a 300 lb Jared. It makes his treatment of the guy even more heartwarming.
Even though the survival dome was going to reset anyways, Commander is willing to make sure the Megalodon is returned to water because he knows his son won't forgive him if he ever did something bad to a shark. And acknowledging that Jared is a pro at wangling sea monsters.