Basic Instructions has a strip where both Scott and a customer find common ground over hating going into Scott's place of work.
Parodied in Adventurers!, when the Big Bad pulls the second type of Not So Different moment on the hero in this strip, and has it fall flat almost immediately since the only examples he could come up with were their similar heights and shared penchant for pointy hair. He admitted that he probably shouldn't have made it up on the fly.
Violetta: Really. So you've completely missed the fact that he's overbearing, self-aggrandizing and certain death to be around?
A much darker version comes later - the main reason the Other is so reviled by pretty much everyone is that she uses slaver wasps to control people, with them having to obey her every order once they have become revenants. Even other characters with Undying Loyalty hate the idea of forcing people to obey. One of the main forms of opposition to the Other come from Baron Wulfenbach, who has spent the majority of his rule gathering and destroying the Other's technology, and has biologically engineered weasels to sniff out revenants. And then he goes and does the exact same thing as the Other has done to Agatha, by implanting a copy of his personality into his son so that he can control his to some extent and make sure that he doesn't help Agatha. This is explicitly called out in-comic by the Other herself. When the Big Bad herself is criticising you, you know you've fucked up.
Not said by a villain, but comparing a Corrupt Corporate Executive to his son: Rollie, of Gene Catlow, explains exactly how Steven Avariss is like his father. It boils down to an aspect of their personalities that could be good or bad, depending on how it's applied.
In Erfworld, Stanley declares that his enemy Ansom rules by "violence and fear" (with "just like me" implied though not admitted), not by "nobility" as he likes to believe. Later, it becomes evident that Ansom and Stanley are both fighting for their respective visions of the Titans' will.
When Elan finally realizes that his father is Evil, he declares that he's no better than his Evil Twin Nale. Tarquin takes offense, deriding Nale as an egomaniac more interested in being the center of attention than a functioning plan for world domination. But as the arc goes on, Tarquin proves to be no different; he continues to antagonize the Order because he wants to be main villain in an traditional hero-son vs villain-father story, which he thinks only works if Elan is the leader, which means Roy and others who could overshadow him must die. He wastes time, manpower and personal favors pursuing this goal, showing himself to be more concerned with being the center of attention than his long-time goal of taking control of the continent.
Torg: We're her family, Riff. This is her home now. She's not going to destroy it anymore than you would ... with your various nuclear isotopes and biological pathogens ... OK, bad example. Actually, it's not! Riff, with all your dangerous scientific experiments, I put it to you that Aylee is less likely to threaten humanity than you!
Strip 1451 demonstrates the underutilized tactic of trying this on God.
God: "What about all those children you killed?"
guy: "They were all firstborn sons of Egyptians."
Strip 4076: What if the war on drugs is a form of addiction?
Happens a lot in Lightbringer, and the titular character quickly becomes tired of it:
Lightbringer:It's the same damn speech I keep hearing. "You're just like me." "We both want the same thing." 'why are you fighting against me?" The Gentleman told me it. The SmilingMan said he used to be just like me. Werres told me we fought the same fight. And now Darkbringer is using the tired old bit.(...) I'm sick of evil people telling me I'm like them.
Also, one interesting example was when Police Chief Eddie Crane tried to arrest Bruiser, former cop turned into Vigilante Man after death of his kids. Bruiser said he knows what Crane did to murderers of his own family, making Crane left him go.
Sarah from Weregeek recently met a pack of non-geek girls and proceeded to make a rather disturbing discovery.
In Goblins Forgath tries to invoke this to persuade his specist partner Minmax that their new snake-girl companion is in fact a perfectly normal and sound being and thus shouldn't be slaughtered for XP as Minmax is eager to do. Hilarityensues.
In Slightly Damned Angels and Demons appear to superficially follow their associated tropes of good and evil, but the more that is learned about the angels, their magic, talismans and how they interact with demons, the more doubt is thrown onto the binary assumption.
On an individual level we have Buwaro's adoptive older brother Iratu and Kieri's twin Kazai, Iratu is leading an invasion that has resulted in hundreds if not thousands of medians dead and brushes it off by saying that the good ones will be sent to heaven and the bad ones to hell, earlier we hear Kazai give a similar excuse to not waste time saving them from said attack. They also both view median life as lesser than the lives of their respective species and and will mindlessly follow what they believe are their gods plans, also both become hostile towards their siblings when they don't think in a similar way though the main difference being that Kazai only did so in a moment of anger and genuinely loves his sister while Iratu doesn't love Buwaro and actually tries to kill him.
And gives us a strange variation in this strip, where Fuchsia, formerly a Depraved Bisexual succubus and Torture Technician for The Devil, in the midst of a Villainous Crush and a High-Heel–Face Turn, listens to her love interest, Criminy, relate a story that could very easily be about Sinfest's main character, Slick, and comes to realize that she has a lot in common with the Damned Souls that she formerly took delight in tormenting. Her response, in a Crowning Moment of Heartwarming, is to sit with the Damned and hold their hands, offering them comfort.
In Drowtales, despite being a Superior Species the drow in particular are not actually that different from the goblin races. Just take a look at how the drow consider the goblin races. Now take a closer look at the drow. Ironic that the ones who consider halmes akin to locusts almost destroyed their own planet for mana-based life a millenia ago, isn't it?
In Advance Wars, there are three main missions in which Black Hole calls this; the most significant is Sonia's A Mirror Darkly, in which she and Lash play a game of chess (with artillery and neotanks, natch), but both of Grit's missions in the Blue Moon campaign section show Lash and Grit invoking this trope, too.
Homestuck: Jade is so frustrated with her newly resurrected dream self that she begins verbally and physically beating her. Then Karkat comes pestering with a "friendly" reminder that this behavior isn't unlike his insulting his past/future self...which she had gotten quite pissed off at him about not much earlier.
Vriska attempts this with Terezi, but given that Vriska has greviously injured other trolls just for fun while Terezi only ever murdered 'bad' trolls or to seek revenge, and given that Alternia is a Crapsack World anyway, it falls flat.
AG: Cause even though you got all these highfalutin morals and fancy reserv8tions, you know as well as me that a killer is a killer is a killer!
Occurs again in the Act 6 Act 3 Intermission when Meenah chides Cronus for bullying Mituna and he points out that she's not exactly a saint either and that in alternate timeline she basically used him to power her spaceship. Meenah struggles to find fault with his argument, but ultimately gives up because she doesn't really care what Cronus thinks.
Another event in that intermission has Porrim deliver a massive social justice rant to Latula, who comments that she seems to be pulling aKankri.
Vriska is introduced to us right away as an overdramatic troll who wants to involve herself in absolutely everything important, even if it means making terrible decisions. Her corresponding pre-scratch troll, Aranea, seems to be much more softspoken, described by Terezi as "4 N1C3 VR1SK4". However, when Aranea decides to try to defeat Lord English by reviving herself and preventing our heroes from creating a new universe, as is the goal of the game, we find that Aranea's and Vriska's motives are very much the same. She ultimately fails and dies. After all this, John later refers to Aranea as "the other vriska", showing just how similar the two really are.
This makes quite a bit of sense when you consider how messed up Mindfang, Aranea's pre-scratch self, was.
The Renavanna and Eytherlia elves of Ears for Elves, according to Tanna after Zalanna pronounces them feral. The unusual arrangement of panels on that page emphasises Tanna's point.
Zalanna: You see, they live in the untamed wilds.
Tanna: So do we.
Zalanna: In a secret, secluded village.
Tanna: So do we.
Zalanna: With border guards dedicated to not letting a soul in.
Tanna: So do we.
Zalanna: They hide away from any non-elf race, threatening banishment to any who commune with outsiders.
Tanna: So do we.
Despite how much Commander Badass dislikes Canadian Guy in Manly Guys Doing Manly Things, they are more alike than he'd care to admit, in tastes of games, enunciation, and even appearance (to the point that they're Palette Swaps of each other). Emphasized in this comic where, despite having three siblings and two children (and though he doesn't mention them, an ex-wife, a love interest, and a surrogate son), Canadian Guy is the one Commander Badass is most drift-compatible with.
It's also hinted that the reason he doesn't try to change Jared is because he's not very much different from Jared, especially around his siblings and army family. Jonesy even literally called him Angel's fuzzy, 300 pound Jared.
MYth: A Promise has Cronus making the comparations between himself and his son Zeus. Both were the youngest child of their generation, choosen and empowered by Gaia. What makes them different is that Zeus never breaks his promises.
KimLurker sees the parallels between him and The HeroJa Wangnan. They both had their dreams toyed with and both have sacrificed a lot of people to get where they are. Ja is shocked and admits the similarity, but this immediately leads to his showing how they are also different, as he shows mercy to Lurker, who'd just brutally killed his friend for not much reason.
We have inter-faction political rivalry of epic proportions. Good luck trying to work out how much lower any of them will stoop in comparison to any other given one. Or, which you'd pin a "Good Guy" sticker on at any given minute: they're all about as good or as bad as each other. Many individuals break down into this, as well: even some truly horrible characters have friends they care about. And, others that seem consistent and honourable one minute will turn around and cut somebody else off at the knees the next.