* From ''very'' early in the comic, [[http://www.girlgeniusonline.com/comic.php?date=20021106 this little note from Phil]].
* Also from the same period, regarding Agatha's missing uncle:
-->'''Agatha:''' Maybe.. maybe he.. he never ''meant'' to come back!\\
''[Adam places his hand on Agatha's shoulder and [[TheVoiceless firmly shakes his head.]]]''\\
'''Lilith:''' Agatha - your uncle loves you very much. Almost as much as we do.
* As Agatha, Krosp, and Othar are leaving Castle Wulfenbach, she takes a moment for [[http://www.girlgeniusonline.com/comic.php?date=20040915 an affectionate "so long" to newly discovered cousin Theo]].
* Early in the story between Agatha and one of the [[http://www.girlgeniusonline.com/comic.php?date=20051010 Jaegerkin]], as Ognian bursts into tears and hugs her, so delighted to have found the master they were looking for. It manages to be touching in a mother-comforting-her-child kind of way, despite being between a mad scientist and one of her family's comic relief monster HenchmenRace. You find yourself going "awww" even though the "child" is over ten times the "mother"'s age, a couple feet taller when he isn't crouching, and ''has razor sharp teeth''.
* A mix of [[CrowningMomentOfAwesome Awesome]], [[CrowningMomentOfHeartwarming Heartwarming,]] and TearJerker in [[http://www.girlgeniusonline.com/comic.php?date=20070209 this strip,]] when Maxim mourns [[spoiler: Lars]] and gives up his own, very beloved, hat in his honor.
--> "He fight vit us Jägers und die for the house of Heterodyne. Dot make him as goot as vun of us. Ve don't leave our own behind. (...) So ven hyu bury him, make sure he gots a hat."
* One from, of all people, Baron Wulfenbach. He watched his son take on an entire army by himself, and brilliantly bully them into submission with a combination of mad science and bare-faced bluffing. To see this he had to be moved despite his life-threatening injuries. His response? "[[http://www.girlgeniusonline.com/comic.php?date=20071203 Anything-- being paralyzed for life-- would be an acceptable price for seeing what I have seen my son do today.]]"
* [[http://www.girlgeniusonline.com/comic.php?date=20090327 A small one]]:
---> '''Gil:''' Ow! Why are you hitting me? ''I love her and I want to help her!''
---> '''Zeetha:''' Now ''that'', I'll pass along.
* Heartwarming/Awesome/Funny in [[http://www.girlgeniusonline.com/comic.php?date=20090805 this episode,]] which is a bit of a MoodWhiplash.
* [[http://www.girlgeniusonline.com/comic.php?date=20090810 Gil's scary look of determination.]]
-->He's ''not'' going to ''die''.
* Adorable and hilarious all at once: [[http://www.girlgeniusonline.com/ggmain/strips/ggmain20091023b.jpg "I'm going to save you both. AND THEN I'M GOING TO KILL YOU!"]]
* Although [[http://www.girlgeniusonline.com/comic.php?date=20101018 this page]] comes off as a set-up for TheReveal with a bit of a TearJerker in the two second-to-last panels, it's actually a bit heartwarming if you look a bit further--to quote [[http://tvtropes.org/pmwiki/posts.php?discussion=0000000000000000000002oy&page=304#7577 our forum:]]
-->[[spoiler:Agatha loves Zeetha enough to go be stupid. Tarvek cares enough about Agatha to struggle to stop her. Violetta cares enough about Her Lady to stop her. Tarvek cares enough about the cousin who "hates" him, and who he supposedly "hates back", to be frantic that she's going into deadly danger. Violetta cares enough about her role as protector and defender to John Wayne up anyway...when she KNOWS she is a "bad Smoke Knight", and KNOWS Zola has already kicked her butt soundly. And Higgs...Higgs "vas beginning to like" Zeetha. Enough to be devastated for her.]]
-->It's a page just chock full of people loving and caring about each other. Each frame is a little jewel of emotional engagement.
* Sleipnir and Theo have been giving us loads of these, such as when the ceiling over their workspace is in danger of collapsing--so Theo handcuffs Sleipnir nice and far away.
-->'''Sleipnir:''' If you die I'll hate you forever, you selfish pig!
-->'''Theo:''' Good! Yes! [[IJustWantMyBelovedToBeHappy Hate me for years and years and years]].
** Another Theo/Sleipnir one--something big is coming for her, but she's still chained to the wall ([[DramaticIrony for her own safety]]). Theo rushes over, but he can't find the key, so he shields her with his body as the danger approaches.
* Higgs is [[spoiler:[[http://www.girlgeniusonline.com/comic.php?date=20110128 postponing Zola-related vengeance to make sure Zeetha's okay.]]]] Awwww.
* Simultaneously heartwarming, [[MomentOfAwesome awesome]] and [[TearJerker saddening]]:
--> [[http://www.girlgeniusonline.com/comic.php?date=20110603 […]I am Castle Heterodyne. My first charge is the safety of the Heterodyne family. All of Europa believes I have failed. And they will not believe otherwise until you are recognized. Publicly. By me. …And you will be.]] [[spoiler: Even if it is my '''final act.''']]
* [[http://www.girlgeniusonline.com/comic.php?date=20110715 "And I am fond of you, professor. Which is why I shall do this quickly."]] A rare moment of Castle Heterodyne NOT being gleefully sadistic.
* For pity's sake. [[http://www.girlgeniusonline.com/comic.php?date=20110817 Give him something to fight for!]] Attached to this moment of IJustWantMyBelovedToBeHappy is that for once, Tarvek actually ''didn't'' see any sort of [[http://www.girlgeniusonline.com/comic.php?date=20110907 political calculation]] in the situation. And Tarvek schemed to...[[http://www.girlgeniusonline.com/comic.php?date=20110909 keep his cousin]], who thought they regarded each other with mutual disgust, out of danger.
** Vole's observation at the end of that scene adds to the effectiveness. Even he, who considers the recent Heterodyne generations to be unworthy of the name (to the point of wanting to destroy them), doesn't dare raise his hand against Agatha in that moment.
* A surprisingly touching one [[http://www.girlgeniusonline.com/comic.php?date=20120118#.VrZV_8ko6BZ comes from Dupree]] and Gil. Dupree may be a vicious little psychopath, but she is completely loyal to the baron and always follows his orders if she interprets them in creative ways. When Gil confronts her on abandoning the Baron, she breaks down crying, pointing out that she tried to go back and save him, but ''failed''. Gil comforts her with a hug telling her that if she couldn't save his father, then no one could. Doubles as a TearJerker.
* The first panel of [[http://www.girlgeniusonline.com/comic.php?date=20120201 this]] update edges into this when Agatha is examining Gil's lightning generators.
-->'''Violetta:''' Did you notice he wrote your name on all the bolts?
-->'''Agatha:''' ''Obviously'' he has too much time on his hands...but I thought it was very sweet.
** It's been established before that the Wulfenbachs put their name on ''everything'' in their machines, the bolts included. This isn't the Spark equivalent of Gil doodling Agatha's name in his notebook, the lightning generators were ''intended'' as a gift.
* [[http://www.girlgeniusonline.com/comic.php?date=20120224 A match made in]] WarriorHeaven.
** Even sweeter, when Gil [[spoiler: saves Vole from the Time Bubble]], he rages in pain [[spoiler: while aging rapidly, turning huge]]. She stares for a moment before being overtaken with joy about the development. While we don't know how Vola will think about the situation, she obviously has absolutely no problem with the development.
* Professor Mittelmind and Fraulein Snaug's weird twisted Spark-Minion relationship: they honestly care about each other and are just so cute.
--> '''Mittelmind''' ''(pleasantly surprised):'' Fraulein Snaug! Astonishing! You're alive!
--> '''Snaug''' ''(happily):'' Whee! And you're still [[OurZombiesAreDifferent a twisted mockery of life]], sir!
--> '''Mittelmind''': Sauce!
* Ladies and Gentlemen, [[http://www.girlgeniusonline.com/comic.php?date=20120718 Tarvek has decided]] the ''hell'' with Wulfenbach and IWantMyBelovedToBeHappy. He's in love and he's courting Agatha no matter what.
* Remember all that [[UnresolvedSexualTension UST?]]. [[http://www.girlgeniusonline.com/comic.php?date=20130320 It's been resolved.]]
** The previous strip containing [[spoiler: the LoveConfession from Higgs]] [[http://www.girlgeniusonline.com/comic.php?date=20130318 is even better]]
* Turns out, Tarvek does [[http://www.girlgeniusonline.com/comic.php?date=20130329 care]] about [[spoiler:Gil]], politics be damned.
* [[http://www.girlgeniusonline.com/comic.php?date=20130726 On the Baron's paper doll,]] attached to one of the outfits is...a beaming little toddler Gil. And there's a cut out version of him to attach to the other outfits as well!
* The fact that for all his rough edges and HeroWithBadPublicity status, the Baron's reign is remembered as "[[http://www.girlgeniusonline.com/comic.php?date=20131021 [like ] some lost golden age of antiquity]]".
* [[http://www.girlgeniusonline.com/comic.php?date=20131202 The triumphant return of Airman Higgs.]]
* [[http://www.girlgeniusonline.com/comic.php?date=20131209 Maxina Agatha Gillina Heterodyne Clay]]. As Adam put it, "When young Wulfenbach sets out to repair something, he doesn't do it halfway." His expression in the top panel is a look seen on many new fathers.
* When accused by the Father Abbot of arranging for Lady Selnikov's arrival as part of a master plan, Martellus [[http://www.girlgeniusonline.com/comic.php?date=20141114 sincerely denies]] any involvement, genuinely taken aback at the thought of plotting against a church.
** Or possibly [[YouAreBetterThanYouThinkYouAre taken aback at the fact that it never crossed his mind to do so.]]
* Dr. Vapnoople really did have an army. [[spoiler: Of ''intelligent bears'' all programmed to obey Krosp, proving he really felt his feline creation would lead.]]
** Martellus reveals the [[spoiler: bears are programmed to obey the doctor's "''masterpiece''". If that doesn't say Krosp's "poppa" loved him, nothing does.]]
* Gil and Agatha [[http://www.girlgeniusonline.com/comic.php?date=20150408#.VSaSLJMkeZY meet for the first time in two years]].
* Klaus [[spoiler:in Gil's body]] finally lays bare to Lucrezia [[spoiler:in Agatha's body]] [[http://www.girlgeniusonline.com/comic.php?date=20150427 his REAL reason for everything he's done since returning to Europe:]]
-->'''Klaus:''' [[SeekingSanctuary Sanctuary]] or not- I will '''burn this fortress and every soul in it''' before I allow '''you''' or '''anyone else''' to '''[[PapaWolf harm my son.]]'''
* On the romance front, it turns out that Zeetha has a way to send messages to Higgs. At a set time each day, she slowly says a message, which Higgs sees on her [[ExpressiveAccessory circlet crest]]. The first message we see? [[spoiler: I. Love. You.]]
* Bangladesh Dupree: AxeCrazy PsychoForHire, who spent most of the first few volumes helping the Baron hunt down Agatha with prejudice. When she and Gil ''finally'' catch up with her following the TimeSkip? [[http://www.girlgeniusonline.com/comic.php?date=20150415#.VsvdjtAm_e4 She can't outright say she realizes something's wrong with Gil, but she hopes that Agatha will be able to fix it.]]
* Gil [[spoiler:rescues Tarvek from the time bubble around Mechanicsburg]] and promptly [[http://www.girlgeniusonline.com/ggmain/strips/ggmain20160311.jpg gives him a huge hug]]. Note when he says "Ha ha! You're fine!" It's in a normal speech bubble, not the hyper-extended spark-use bubble. For a brief moment, he's just Gil again.
** In the same vein, Gil also talks normally while [[spoiler: Tarvek]] takes a bath and when he gets the book from Agatha. He can't fight against it all the time, but finding those he cares for interacting with him (in some way) seems to bring him back for a bit.
* Crossing over with Awesome: Dimo reveals the reason behind the Jägers' "absence" from the Heterodyne stories: they were hated, and the Boys wanted to break from their family's reputation. When some were caught following, they were all ordered to remain in Mechanicsburg. Dimo thinks that Agatha should think about that. [[http://www.girlgeniusonline.com/comic.php?date=20160708#.V39vDHlTGUk Here is her reply.]]
* In ''Literature/AgathaHAndTheClockworkPrincess'', Klaus describes Punch and Judy as "the two greatest people I have ever known." Heartwarming enough on its own, but more so when you remember that the most obvious people to compare them to would be the Heterodyne Boys, who everyone else sees as the greatest people the world has ever known.