* Dracula threatening Dr. McNinja through Gordito does not work. Why? [[http://drmcninja.com/archives/comic/11p35/ Because the doctor believes that strongly in Gordito's abilities and he's right.]]
* The zombies from ''Revenge of the Hundred Dead Ninja'' have enough humanity left to remember what was most important to them. We see one such zombie make it to his daughter's school play, tearing up joyfully. [[CrossesTheLineTwice Whilst eating the guy next to him.]]
* [[http://drmcninja.com/archives/comic/21p28 This.]]
** [[spoiler: SEAN MCNINJA DOES NOT LIKE BEING HUGGED PEOPLE.]]
* [[http://drmcninja.com/archives/comic/21p46/ "You didn't pack enough."]] May double as a TearJerker.
** [[spoiler: Mitzi's]] expression and the subsequent hug make it doubly so on the next page.
* [[spoiler: Yoshi telling Dr. McNinja that he's happy that the doctor is alive. Heck, McNinja saying he's happy that Yoshi's alive counts as well]]! Considering that these two have had a rocky relationship in the past, only ever working together when Gordito is in trouble, that the both of them are glad to see each other alive and well is definitely a nice touch.
* During the montage of various scenes after [[spoiler:the humans won the war against the dinosaurs]], we finally get to see [[spoiler:Gordito and Yoshi reunited]]. The look on that raptor's face? Yeah, he missed [[spoiler:his human.]]
* When [[spoiler:Ron, Steven, and the citizens of the Radical Lands arrive in the world, King Radical is just so overjoyed to see them. As terrible as ''how'' they arrived is, KR is seeing his friends and people for the first time in possibly years after mulling around in a considerably blander world. Also since the Radical Lands are dying, them appearing means that he's saving lives.]]
* How does Dr. [=McNinja=] celebrate [[spoiler:defeating King Radical's plan]]? By calling up a pizza place [[spoiler:to get the Friend Brothers back in business]] as a way to [[MustMakeAmends make amends]].
* [[spoiler: The good Doc MercyKilling his own mentor Ben Franklin, stuck on the Mortal Plane as a headless horseman by finally dealing with his UnfinishedBusiness. Just buying a pizza he promised to take him out to celebrate for.]]
* The last page of "Why a Gorilla?" has two: Dr. [=McNinja=] defending Judy against a rude patient and when she thanks him, he responds in sign language.
** The whole story finally shows Doc and Judy communicating with each other, showing us why Judy puts up with the crap working with Doc puts her through, and that the two really are friends.
* Dr. McNinja is largely unaffected by the Negazone, an amalgamation of all the worst fears to every intruder trapped within. Unaffected, that is, until Negazone!Gordito shows up and tells the doctor that he is a bad role model.
** After some brief resistance and denial, Dr. McNinja finally concedes... by saying he'll have a talk with Gordito when it's over and see what he needs.
* Doc's meeting his Grandfather for the first time as a kid has some sweet moments considering half the story he's trying to teach Doc to justify murder.
-->'''John''': Hanging out with grandpa... that means ice cream for breakfast?
-->'''Doc''': Yes it does.
* ''The Doctor's Final Thoughts'' on ''The End: Part 1'' concludes with him finally seeing a patient who's appointment had been pushed back numerous times, despite standing in the burnt remains of his office.
* The ghost wizards' reunion. The ghost wizard that fought Dr. McNinja in his youth was being sincere after all.
* Mitzi McNinja, the one person in Dr. McNinja's life who was always critical of his decision to become a doctor, is finally [[http://drmcninja.com/archives/comic/33p13/ ''proud'']] of her son.
** Another heartwarming moment: the universe has turned its back on McNinja, according to [[spoiler: the ghost wizard]], so are we about to see him bust into the villains' lair for one final showdown, completely outnumbered, all alone? [[http://drmcninja.com/archives/comic/33p12/ No. Not in the slightest]]. Or at least, [[spoiler:not at first. It gets completely reversed when his own family and friends betray him, with him not knowing why.]]
** [[spoiler:It turns out it was to save Gordito, and even then it's shown that they had to tie up Martin because he didn't want to betray the Doctor. And judging by their faces, his parents aren't exactly happy about betraying him]].
* Doc [[http://drmcninja.com/archives/comic/33p76/ finally gets through]] to his poor confused cloned self and convinces him that he's just a little out of his head, not dying of CloneDegeneration.