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 (—who put himself in front of Hank first—). Now that's a statement.
Brock's threat to Phantom Limb in "Victor. Echo. November." about staying the hell away from the Ventures, even after Limb had just reminded him what the Guild would do to Brock if Limb was killed.
Brock: Let me give you a warning: if you ever sick your goons on the Venture family - MY family - I will-
Phantom Limb: Yes, of course. Scary-scary. It won't happen again.
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!!"
Rusty trying his hand at songwriting for an autobiographical musical. It might seem like a self-aggrandizing get-rich-quick scheme, and it is... but Dr Venture just looks so uncharacteristically happy singing and playing the keyboard.
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 worrying about the boy when they can just make another clone of him.
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.
She also seems to be rather accepting of their "relationship" which is quite progressive for a woman who was concerned about Action man's adopted son being interested in Rock'n Roll.
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."
When Dr. Killinger gets the Monarch and Dr. Girlfriend back together.
Love is not private. Love is to be shared. I've locked you in. Neither of you may leave until you have reached compromise. Good luck, and may love show you the way. Say goodbye to all your pretty children for me.
When Dean calls Rusty "Daddy" and Rusty doesn't correct him; he even refers to himself as such. Most dad's would not like their sons to use such an affectionate nickname.
The ending of the episode "Assassinanny 911." We spend the entire episode being told by Molotov Cocktease that the Venture family essentially stole Brock Samson's life, and watching Brock relive the action and adventure of his old super spy days. At the end of the episode Molotov offers Brock the chance to leave his current life behind and return to being a super spy full time. He responds by smiling and saying "Sorry, Molotov, but... Go Team Venture." (Incidentally, this is also the first time in the show that Brock himself actually used the Venture Family's Catchphrase.) This is when we realize beyond any doubt that, as much as Brock might be annoyed by the Ventures from time to time, he does think of them as his own family, and he wouldn't give them up for anything.
In Assisted Suicide season 4, when using Dean to enter Doc's mind fails, he walk dejectedly over to his brother, who immediately puts his arm around him for comfort.
In the same episode, while waiting for doc to wake up Brock and Hatred share a moment while talking about Hank letting off two good leg shots; the proud look on Hatred's face sells it. Immediately after wards, both hear that something is wrong with Dean and rushes out to help him.
At the end, Brock and Hatred are fighting over the responsibility of the boys, Rusty comes out and tells them with no uncertainty that they're his problem. He then starts handling them without missing a single beat.
Rusty's and Hank's moment together after the credits was rather sweet considering the two rarely get a moment like that.
In SPYNX Rising season 5, Doc shows a brief over protective father moment for Hank.
For a moment in Venture Libre season 5, Doc asks about Hank and Hatred says he's dead. Doc looks panicked until Hatred assured him that it was just his watch that was dead.
A small one, but in O.S.I love you, season 5 Hank's strength suit is stolen and as a result, he has to retrain his muscles. Col. Gathers offers sympathies over the loss of his breasts. This is heartwarming considering he was threatening to shoot him earlier.
In Handsome Ransom, Doc is reluctant to do anything about the ransom until Dean cries out in fear. Doc then tries to offer the Monarch anything in his lab as he doesn't have ten million dollars at the time. Then when trying to get Hank back later, you can see that he is calling everyone (including the brother he hates) to get the money. This shows that despite Hank getting under his skin all the time, he does want him back. (At least a little bit.)
Hatred, despite being surrounded by henchmen with guns, the first thing he notes is that Hank Who was “saved” by Captain Sunshine earlier was missing.
When the second trade is going down, Doc is immediately able to see though the Monarch's trick because the imposter wasn't wearing Brock's coat, which he states wild horses couldn't get him out of. This shows that he knows his son at least a little. (Or that he tried to get him out of the coat and failed.)
In The Buddy System season 2, after meeting Dermott, Hank is so happy and runs up to his father to ask if he can show him his room. Doc however is rude to him and even hurts his feelings. Seeing this, Brock immediately asks Hank to help him with his judo lesson to cheer him up.
Brock gets another small one when he lies to the monarch about Doc missing him as a nemesis.
At the end when Dermott is leaving, Hank asks if he could call or do what friends do. Dermott immediately responds that they can hang out. Hank looks so happy at the end.
In the first episode, the monarch actually tries to be nice to the boys after capturing them, sympathizing with them about the fact their father couldn't care less.
A bit of fringe heartwarming(or YMMV); In the first ep of season 2, you see Brock tracking Rusty down, after the boys die. Most of it is probably because it's his job, but it could also be seen as he misses the boys and wants Rusty to awaken the next set of clones so they'll be back.
Doubles as a moment of Awesome; After wandering around with the other boy adventurers and talking to Dr. Z, Venture states that he wasn't alone and that unlike the others, he had grown up and had a family. He then states that it was time he got back to them.
In 'I know why the Caged Bird Kills' Brock is searching for the boys and comes upon a dumpster. He looks terrified until he discovers the watches. Later in the same episode, he shows a small bit of papawolf-ness when he states that he'll kill Myra if she hurts the boys. (note that Brock's one rule is never kill a woman or child.) It's always heartwarming to this Troper when Brock shows his protectiveness for his family.
In S 1 E 3, H.E.L.P.E.R is seen taking care of Rusty, tucking his in and everything. What makes it even more sweet is that it's implied he's been doing this for Rusty's whole life. It turns to a tear jerker when he finds the plans for the new robot. And even then, he takes a picture of him and little Rusty with.
Later, Doc actually apologizes to H.E.L.P.E.R. (considering this is Doc, this is a big step.)
Doc:I... Rusty needs your help.
In the same episode, the Hench all get together and have a swell time, until they're ultimately killed.