Dr. Mrs. The Monarch, when she dressed up as a cheer leader and gave 21 a cheer to well... cheer him up. She later revealed that she and 21 have more interests (namely, Star Trek) in common than he would have thought.
In "The Invisible Hand of Fate!", Brock and Pete White get one: Brock grabs a memory-wiped, unconcious Billy Quizboy and sneaks him out of the OSI. Cut to Pete White in the middle of the desert, sunburned to shit (Remember, he's an albino, that shit is easily fatal), and Brock pulls up to him, gives him a little speech, throws a duffel bag at him... Containing Pete's best buddy in the world, Billy, whom he clutches to his chest and weeps for joy. The music just seals the deal.
In the same episode, there's a scene where Pete thinks he's signing Billy up for another quiz. Turns out, it's a dog-fighting match. Even though it causes Billy to be disqualified and thus causes the huge fight that eventually splits them until the aforementioned scene, the fact that Pete apparently jumped into the ring to try and rescue Billy, risking his own life and limb (literally; this is how Billy lost his hand), is honestly rather touching.
The Venture Bros. has another example of an atypically heartwarming message at the end of the episode "ORB" where Rusty tells Billy that he trusts his father's judgement:
Dr. Venture:He may have been a horrible father, but he was a great scientist. If my father hid this, he had a good reason.
For all his resentment of his father, In Twenty Minutes Till Midnight" when Rusty sees his dad appear through a portal he is reduced to tears, begging his him to stay when he is about to leave. Of course, that really isn't his father but it shows that Rusty still loves his dad.
Jonas Venture Jr., otherwise more likable than his brother, edits together old clips of their father to make it seem like a clip of their father saying his greatest invention is his son is talking about him (Jonas Venture Jr.). It is of course talking about Rusty, who left before watching it. Yes, it's suitably corny, but still.
In the third season finale, after Sargent Hatred leads all of the boys' clones into a doomed battle where they get sliced up by lasers, Rusty follows up with possibly his one act of genuine parenting in the whole series to date.
Dr. Venture: Calm down, Hank. You only live once.
You all seem to be forgetting the episode where Rusty failed to fix his shrink ray. After he bemoaned himself as a failure, Billy Quizboy showed him his Rusty Venture lunchbox, reminding him that at one point, he was the premier child adventurer.
This troper was moved by a moment when Prof. Impossible was set to shoot chemically-induced human bomb Hank to prevent him exploding - Rusty positions himself in front of Hank, determined to find an alternate method. Granted, he may be motivated to show up his old teacher, but still...
Hell, it's not even Hank he positions himself in front of, but Brock. Now that's a statement.
The end of the first episode of Season 4:
Hank: Why did you leave me?
Brock: Hank, I'll never leave you... but right now, these guys need me a little more. You can share me, Hank, can't ya?
In "Operation P.R.O.M", Brock is speeding off to protect the Venture family after Molotov reveals that the escorts attending the prom are her Blackheart agents waiting to slaughter those attending at midnight. Even though his bodyguard duty has been passed on to Hatred, Brock is noticeably scared for the people he considers family as he races to the compound, knife in hand. He doesn't even take a moment to mourn Molotov's apparent death.
In "Every Which Way But Zeus", Hatred and the boys use some voice-altering toys "kidnap" Rusty because he expects to be kidnapped along with everyone else. He asks that they not torture Dean, but doesn't seem to mind them killing Hank. He later explains that he doesn't love Dean more. Except that he knew they weren't going to kill Hank, and if they're gonna pretend to torture someone, it might as well be Hank. Hanks asks if it's because Hank is tough while Dean is a wuss, and Rusty says that Dean has the idealism of "Rusty Venture: Boy Adventurer". He actually likes the whole superscience thing. Hank was thrust into "this life" and rebels against it, just like Rusty did.
Rusty: He's a Venture. He'll never shake it.
D-19's last moments were spent hugging his father— the only thing he ever wanted his entire life.
Dr. Orpheus, Jefferson and the Escort hugging Gary after he lets 24 go. Even if they do think he's crying for a totally different reason.
That proud little smile that play's across Brock's face as Hank ecstatically proclaims "I GOT LAAAAIIIID!!"
From the Christmas songs, there's Monarch and Dr. Girlfriend's duet of "Fairytale of New York", especially when they sing about their dreams near the end.
Also in the Season 4 finale, when Dean and Hank talk Dermott into joining them for a "Go Team Venture" as they go off to get Triana back despite the fact that none of the three of them know that Dermott himself actually is a Venture by blood.
Hell, Dermott agreeing to help them in general. Sure, his advice is stupid and makes it readily apparent that he's a douchenote he thinks dressing Dean up in goth clothing will make Triana cream herself but he clearly means well.
Nicki Fictel's brief appearance during the Shallow Gravy special, talking about when Dermott was a kid, and would sing Spice Girls songs on the couch. Might seem like a sister just trying to embarrass her brother, but is rather heartwarming when you realize it's actually a mother reminiscing about her son. Especially since she mentions how adorable he was.
The ending of "Return to Malice" tugged my heartstrings. After 21's plans all came busting down, he is left downtrodden in his childhood treehouse. The Monarch, disfigured after 21's new cook gave him food he unknowingly was allergic to and can't make the big supervillain magazine photo shoot, offers him some comfort about the night of failing to torture Hank and Dean for info of 24's death. Then he orders the treehouse to burnt down. A second time in the same ep was with Rusty's and Dr. Girlfriend bonding over waiting for a hostage exchange that never happens. It compounds the idea that these are just two gifted scientists with a lot in common, just bonding.
Likewise, the ending of "The Revenge Society" with Dean being revealed to be the rightful heir of the Guild of Calamitous Intent and bestowing it back to David Bowie. Also his father/son moment with Rusty was sweet too.
When Hank (in his Batman costume, no less) runs off to save Dean from being forced to marry Baron Underbeit and Brock's lip quivers as he watches. Dr. Venture even mocks him for being proud of the little brave idiot.
The Stinger in Season 4 of Hank, half-sleep, wandering into the kitchen and not even noticing that Brock is sitting at the table covered in blood eating a bowl of cereal. What really seals it is that he gets a glass of water and walks past him again, saying, "Night, Brock" and Brock kindly replies, "Night, Hank." Then we hear a glass break from the other room and Hank yells "BROCK?!"
Triana's and Dean's mutual breakup at the Stinger of the season 4 episode "The Better Man"
In A Very Venture Halloween there are actually two. The first is when Doctor Venture after finding out that Dermott is his kid, starts treating him as his son. The second is at the end when Dean finds out that he and Hank are clones, which distressed him greatly, and he decides not to tell Hank.
Dean and Ben's entire chat Ben tells Dean that he's a clone and when he (understandably) freaks out Ben assures him that he's still Dean and not some science project. Ben also states that Doctor Venture loved his sons so much that he refused to even let death take them away from him and started his cloning project in the first place as a way to protect them, comparing the whole process to "A band-aid for a really big boo-boo!"
There are two other in the special. The third would be Sgt.Hatred's devotion to the holiday (He bought full bars of chocolate for any trick or treater who made it past the compound's defenses) and Orpheus' master calling out every person at Orpheus' party for not heeding Orpheus' warnings of letting the party go out of control and raising zombies when there are children about and to that off, he calls Orpheus his favorite student in front of all them.
And right after that, Dr. Orpheus delivering what, as far as this troper has seen, could be the first legit true meaning of Halloween aesop that does the holiday justice, being s thoughtful and meaningful as Christmas; Halloween is the night we discover who we are.
Doubling as a Crowning Moment of Funny, the stinger of "What Color Is Your Cleansuit" has The Monarch and Dr. Mrs. The Monarch sitting on the floor of the Cocoon together, high, laughing, and The Monarch turns to her and says "You're, like, so awesome. You are, like, my best friend."
That same episode has Dean befriending a girl named Talia. They become pretty close, so much she trusts him enough to show her mutation to him. Dean doesn't even react in fear so that is something.
The Monarch still believing #21 was still working for them and even them watching Game of Thrones together was good somewhat.
Dean returning H.E.L.Pe.R to his pre-Walking Eye form.
After Gary feels useless and upset, having done more harm than good, Brock tries to cheer him up by giving him his cross bow, the very same cross bow that he didn't want Gary using (or at least not to borrow it without his permission).
Sgt. Hatred trying to cheer Dean up (in "SPHINX Rising") and it actually looks like he's succeeding. He gets the wrong idea about a number of things, but one of his comments accidentally hits very close to Dean's actual issues and Dean appreciates it.
Sgt. Hatred: Dean, growing up is hard; it's supposed to be. You're not like anyone. You're Dean... and you're the best Dean.
Dean: Hmm. (smiles) That... almost helps.
At the beginning of "Spanikopita", Rusty's slideshow shows a picture of Brock, Hank, and Dean cheerful together at the beach. It shows that Brock will always care for the boys even if he can't be with them, and it's really heartwarming that the possibly Ax-Crazy bodyguard has a soft spot.
How happy Rusty is while on the island is heartwarming in of itself.
The origin of the Spanikopita festival: Georgio and a group of his associates were pirates who were looting the X-2 and accidentally took Rusty (who was hiding in a trunk at the time playing Trojan Horse). They initially hold him for ransom, but after days of not being able to reach his father and of the boy crying, Gerogio made up the festival of Spanikopita to make the boy happy, eventually forgetting all about the kidnapping, and happily kept the charade up years later when he returned and every year since.
Though Jonas Sr. does partially redeem himself after the credits. He immediately sees through the charade but runs with it long enough for Rusty to be ushered out of the room with a head full of happy memories before brutally beating the people who obviously kidnapped his son.
Slightly lessened when you realize it probably had more to do with someone stealing from him, rather than it being his son. Still, it's by far his best actions as a father so far.
In O.S.I. love you, Hatred tells Hank to protect his family and charges after Molotov Cocktease. Hank responds by using his strength suit to save Hatred from her with a "you kind of are my family, uncle 'Vatred'".
In Momma's Boy, Dr. Venture's concern over his 'boys' when finding the stuffed bear, as well as his commitment to saving Ted.
His encounter with "Ted" definitely counts as this.
Dermott calling Dr. Venture "Dad".
There's even a sweet brotherly moment between Hank and Dean when Hank cheers up Dean after discovering Myra isn't really their Mother.
Hatred continues to show concern for Dean, this time believing that he may be going through anorexia or some serious girl trouble. His concerns are completely wrong most of the time, but still, his heart is in the right place.
A few in the season 5 finale:
Hank realizing that the woman Action Man has been pining for is actually Billy's mom and arranging the two to be reunited.
Colonel Gentleman and Action Man becoming roommates. Even more so is that Billy's mom is coming along, suggesting that Billy might have the Action Man himself as a step-dad.
It's a small moment, but when Billy's mother (who thinks Billy and White are a couple) comments on how Billy described White as handsome to her, White's response ("You said I was handsome?") sounds genuinely touched.
When Sgt Hatred accidentally shoots the Flying Cocoon down, he tells Gary that even though he's angry at him for betraying him note It was just a ploy by the Moppets he still warns Gary to get to safety.
Dean finally tells Hank that they're clones. Hank is actually happy to hear this, saying it's all part of being a Venture. Dean smiles and accepts what he is.
Even before they have that revelation, there's Hank expressing his concern for how down and upset Dean's been all year. You can tell he's really concerned about his brother.
Hank: You've been a mess this whole year, man. You've gotta tell me what's eating ya."