Family Guy: Stewie realizes he's not so different from one of his "potential siblings" when one of them mentions that he too hates Lois.
American Dad!: Subverted in "Weiner of Our Discontent" when Roger and Stan find that they both like to feel important:
Roger: We're not so different, you and I.
Stan: Yes we are. We're night and day. Except for in this specific instance.
Also Stan belittles Steve for being nerdy and unpopular, while flashbacks reveal that he was just as nerdy and more unpopular. Indeed, a major facet of Stan's character is how he wants Steve to be cool and popular like he never got to be (not becoming athletic until college), and Stan gets very upset whenever he discovers he is not liked by people, and is desperate to be accepted among his colleagues at times because of his past.
Played straight when Stan kidnaps the children of a lesbian couple. When he hears them fighting in the backseat, he realizes that they are no different from his own kids.
Played straight and subverted in the sequel, The Legend of Korra. After Tarrlok puts the city under martial law and arrests innocents Korra storms into his office, pointing out how he's simply using his abilities and powers to intimidate others. Tarrlok points out that's exactly what she's here to do, and how she goes to the exact same extremes as him. Although initially wounded by his claim, she throws back that he's no different from Amon, the Big Bad that he's opposing. Its a subtle foreshadowing for how Amon and Tarrlok turn out to be brothers.
Cartman isn't the only person Kyle puts in danger. He almost had HIS OWN BEST FRIEND killed by Puff Daddy so he can get Stan's vote for his candidate and then he got even madder at Stan for voting for Cartman's Candidate. He was also willing to send Cartman's entire Pirate crew to their death in Somolia (which included classmates such as Butters and Clyde). This is something Cartman is expected to do, not Kyle. What the Hell, Hero? indeed.
In a later episode, Cartman pulls the Not So Different speech on Cthulhu. Think about that for a second....
In the finale of the second season of Justice League Unlimited, the heroes face Alternate Universeevil twins of themselves. Superman's evil twin taunts him as being Not So Different from him: "Power corrupts, after all, and who has more power than Superman?" This is followed by Superman following the trope exactly by shouting: "I'm not like you! I'm nothing like you!"
Plasmius: Sneak attack — very good, Daniel. You're getting more like me with every battle. Danny: I am NOTHING like you! Plasmius: Oh, you're not? Using your powers to get back at people you don't like? Throwing the first punch? You're more like me than you know.
Ben 10 and Kevin 11. While the former type was pleasantly averted in their Forced Prize Fight episode, the latter type started from Kevin's first appearance:
Ben: (under his breath) You don't care about anyone but yourself. Kevin: You talking about me? Ben: No. I'm talking about me!
In Secret Of The Omnitrix, Azmuth is shown to be immature, selfish, and kind of a jerk, but he's ultimately helpful when he really wants to be... Kinda like Ben, really. When he asked Ben if he wanted to learn about the Omnitrix like a "true hero" would, Ben said he didn't want to, Azmuth didn't tell him the code, but, he did say:
Ben: *furious* Did you forget? This isn't about fame! It's about helping people!
Julie: You are talking about him, right?
In the Grand Finale of Ultimate Alien, Vilgax of all people claims he and Ben aren't so different since they both use power to impose their will on the universe. Vilgax attempts to corrupt Ben into being a tyrant just like him and it almost works.
Kim and Shego of Kim Possible after the events of "Stop Team Go."
Slade is obsessively fond of doing this to Robin, because he wants to make Robin his apprentice. It always makes Robin go into a frenzy of rage, which is always fun for Slade, who just clearly enjoys messing with his head. This was the premise of the "Apprentice" episodes. Robin ponders near the end, "Focused, serious, determined...as much as I hate to admit it, he and I are kind of alike. But there's one big difference between me and Slade — He doesn't have any friends." Slade even manages to do this when he's dead in "Haunted" by making Robin act crazy and violent through drugs. He later taunts him by referring to them as "friends" when they team up in "The End".("I'm NOT your friend!" - because he doesn't have any, remember?) Slade is not all that different from Robin's mentor Batman, with the key difference there being that, while they are both cold and meticulous, Slade is cruel and self serving while Batman is selfless and compassionate behind his ruthless exterior.
An even worse example occurs in "Masks". When Robin tries to justify to Starfire why he didn't tell trust them enough to tell them he was Red X, she sadly tells him that he does indeed have a big thing in common with Slade: Neither of them trust anyone.
Brother Blood tries to do this to Cyborg, but it's not as effective as with Robin, because Cyborg is marginally sane. In fact, it's Brother Blood who takes this the most seriously, to the point that he makes himself into a cyborg to prove his point. The hero's response? "You look like a psycho!"
In "Forces of Nature", Beast Boy realizes Thunder and Lightning are the same as him due to them playing pranks, thinking they're harmless, and never realizing they could cause real harm with it and getting their friendships ruined. Similar to how Beast Boy's friendship with Starfire almost got jeopardized by this, Thunder has a similar situation when he tried to stop Lightning from doing more destruction.
In The Batman, villains try this on Batman with increasing frequency as the series goes on. To his credit (and the misfortune of said villains), Batman proves quite capable of rationally explaining the key differences while he beats the snot out of them.
Then again, while it's rare for a hero to come to this conclusion about himself without any prompting at all from the villain, Batman did so in the episode "The Big Dummy". Alfred was trying to convince Bruce to expand his social life online, and he had actually met a woman named Becky who he promised to meet. As Batman, in the main storyline, he confronted Scarface, and when learning that Arnold Wesker and Scarface were clearly a case of a Split Personality, where Scarface was the dominant personality, he started to wonder if he and Bruce Wayne were similar. If Batman was his dominant personality, he wondered if he could have any true relationship, because Bruce was nothing more than a lie. (At the conclusion, he decided against it, telling Alfred to meet with Becky and apologize. Becky asked if Bruce was married, and Alfred told her he was - to his work.)
One episode of Batman: The Animated Series involves a Japanese ninja stealing the secret of a "deadly touch" technique and facing off Batman for a climactic fight. Batman, himself trained as a ninja, is forced to hear the villain claim this trope. In response, he tells the guy that today, he's fighting as a samurai not a ninja. (Later, when Bruce talked to his sensei about it, the old man put his doubts to rest, denying that Batman was anything like a ninja at all, pointing out that he had tried to rescue his foe and refused to use "deadly touch" technique himself, despite knowing how to. In other words, Batman had the one thing a ninja lacks: honor.)
In Mighty Max, Norman confronts the semi-immortal that slaughtered his village centuries ago. Norman eventually defeats him and has him held over an effectively bottomless chasm when the villain, having a moment of Genre Savvy, triumphantly invokes this trope with the standard declaration of "If you kill me, you'll be just like me!" Norman just looks at him for a moment, before calmly stating, "I can live with that" and dropping him. Aversion from the typical in that Norman never evinces a single bit of guilt over doing so, but then, he was never exactly the touchy-feely hero type in the first place.
This concept takes a serious twist in the Codename: Kids Next Door episode "Operation: M.A.U.R.I.C.E.", where it's combined with You Can't Fight Fate. When it appears that Maurice has sided with Cree, Numbuh Five is almost ready to give up, consigned to the fact that she'll likely end up just like her sister, given the fact that she's nearly a teenager already. And Cree almost seems happy that Numbuh Five thinks this way, possibly thinking that reconciliation between them might be possible if that happens. As it turns out, however, Maurice is actually a Fake Defector who has secretly continued to support the KND after everyone assumed he was decomissioned. After he trusts Numbuh Five with this secret to ensure that she never gives up, she realizes that she can Screw Destiny, and not turn out like her sister at all.
Subverted in an episode of season 2 when Phantom Limb attempts a Not So Different speech on Brock Samson, only to have him interrupt it.
Phantom Limb: We're not so different, you and I-
Brock Samson: Yeah, I don't need another "We're not so different" speech, I get those a lot.
Dr. Girlfriend mentions this trope once, remarking that the Monarch and Dr. Venture have a lot in common. She does want this whole rivalry thing to stop; at least once, The Monarch (having been too obsessed with Venture to get a proper anniversary present) tries to pass off his normal bring-Venture-to-his-knees thing as the anniversary present (Dr. Girlfriend was appropriately incredulous at the notion that The Monarch accomplishing goals that were utterly meaningless to her made a good anniversary present).
Further explored by Rusty and the Monarch themselves in episode The Devil's Grip, where they compare how messed-up their lives are (Jonas Jr. and the Moppets are taking over Rusty's and the Monarch's lives respectively, the Monarch's wife becoming a member of the Council of 13, much to his chagrin, and Rusty's old archenemy being his bodyguard).
In The Fairly Oddparents with Remy and Crocker. Timmy did Crocker's fairy spaz when he went back in time.
Timmy: Fairy Godparents!!! Cosmo and Wanda: (smack and hit him) Timmy: Thanks for not using the oar.
When Timmy met Remy, Remy asked for him to wish his fairies away. Timmy said "You know what stinks about you, Remy? You're rich, you got godparents and you're still miserable. I know, at least, that I'm happier than you, Remy." Later, he says:
Wanda: What's wrong, Timmy? Timmy: (as a dragon) I felt sorry for Remy. I wish I could help him. Wanda: We can do that. Timmy: (as a dragon) I wish Remy could spend more time with his parents.
Also, Norm the Genie did it really subtly in 'Genie Meanie Menie Moe':
The Not So Different is in the choice of words. He chose to say 'out-jerked' instead of outwitted or something like that, which meant he acknowledged both he and Timmy were jerkasses.
Or perhaps he was talking about the Lawyer Timmy wished for.
Mama Cosma and Big Daddy also have this the first time they appeared together. Both of them can't stand who their child happens to be married to and that they tried to separate them which it ended in failure for both of them. This sparked a relationship between them.
The Dark Lord Chuckles the Silly Piggy tries this against Dave the Barbarian. It ends up as a spoof of this trope.
Chuckles: We aren't so different, you and I. We are but twin sides of the same coin. Dave: Uh, no we aren't. Chuckles: ... You're right! What was I thinking?
A rare positive example is displayed in Transformers Prime. Ratchet, who's known Optimus since before he became Optimus Prime, notes that the human Jack reminds him of how Optimus used to be when his name was Orion Pax.
In Beast Machines, when Rattrap agrees to defend Megatron for a night in exchange for weapons (It Makes Sense in Context), Megatron tries to entice him to change sides by saying "You have the makings of a fine Vehicon." Rattrap eventually defies him, saying "Not from where I'm standing".
In a later episode, Optimus Primal intends to use the Plasma Energy Chamber to shut down all technological systems on Cybertron. Cheetor points out that this is no different to Megatron.
In Turtles Forever it's shown that the 2003 and 1987 worlds are very different from each other, but, as the 2003 Shredder says...
The Shredder: Two turtle teams from two turtle worlds, different in so many ways...but deep down, there are similarities.
Also, the Shredders. Even though the Utrom Shredder is the most dangerous Shredder presented, he comes out from the Technodrome and into the open when the Mirage Comic Turtles accuse him of cowardice, a ploy the 1987 Turtles pulled on their own Shredder. As 2003 Leonardo says...
Leonardo: If there's on constant in the universe, it's the Shredder's big, fat ego!
Elise in Dan Vs.. is Dan's biggest critic but is also the one character who is just as ruthless when it comes to pursuing revenge. In the first episode, she shares Dan's grudge against New Mexico. In the childhood flashback explaining why she hates the state, she even let out a Skyward Scream just like Dan does everyepisode.
The resolution to the first Lenny & Sid video, "Love Thy Neighbor". Sid really wants to be Lenny's friend, but Lenny doesn't want it at first — but at the end, Sid stands up for Lenny, which helps him realize that he and Sid can be friends despite their differences.
In Moral Orel, Unhappily married Clay and Bloberta both had a loving relationship with one of their parents, but the other was much colder with them (mother and father, respectively for Clay; the opposite for Bloberta). We also find out during the former flashback that Clay was a lot like Orel when he was a kid and young man, and both were victims of abuse.
In Total Drama, resident Alpha Bitches Heather and Courtney gave very different first impressions at the start of the series (the former establishing her snobbiness from the start and the latter acting nice early on); however, both have very dominating personalities, taking the leadership role within their respective teams in the first season. Their personalities especially clash in World Tour, as both are on the same team. Also, both Heather and Courtney are despised by most, if not all, of their fellow castmates for their antagonistic and selfish ways.
Courtney and Duncan are also this. She berates him frequently for being a selfish, unrepentant jerkass- but she's exactly the same way, except that he's Chaotic and she's Lawful.
This is the basis of Alejandro and Heather's rivalry, and the reason they team up; they're both vain, backstabbing assholes, but they have exactly the same motivation and mindset, making it easy for them to work together (although they mutually agree to betray their alliance once the other contestants have been voted off). They also share a mutual disdain of the other contestants, and gradually evolve into Worthy Opponents.
In All-Stars, this is likely why Alejandro is quick to forgive Heather for her manipulation of him in the previous season. He wouldn't have done the same thing to her, specifically- but he has to many other people, and understands perfectly why she did it to him.
On Goof Troop, Pete and Max loathe each other most of the time, but they have more in common with each other than with anyone else on the show: they're both ambitious leaders who are self-centered and prone to using other people as means to an end, and they're both far better at coming up with ideas than thinking them through. They'd never admit it though, except in "O, R-V, I N-V U" where their similarities lead them to build such a strong bond that a Why Are You Not My Son? situation arises with Pete's diametrically-opposed son as the reject.
In Generator Rex, the cyborg Gatlocke tries this line on Rex, while they're having a swordfight atop an out of control truck heading toward a cliff. Just before the truck reaches the edge, Rex retorts that there is a major difference between them: Gatlocke can't fly.