An interesting variant occurs during the "Acts of Vengeance" crossover, where Magneto decides to ignore the stated purpose and kill the Red Skull. Red Skull launches into a Not So Different speech, essentially taunting Magneto about the fact that his quest for mutant supremacy is quite similar to the Red Skull's own ideology. In the end Magneto spares his life but seals him inside an underground room filled with food and water.
Or Cyclops and Prof. X. After taking charge of the X-Men Scott has begun to keep secrets and make unilateral decisions, the same things that made him kick out Xavier.
This came to a head in Avengers Vs X-Men, where a Phoenix-possessed Cyclops killed Xavier after trying to conquer the world and make it into a mutant Utopia. Now he's on the run and leading his own team of mutant outlaws.
Then theres Emma Frost to X-23, who explains to the latter the reason she wants her to leave Xavier's Institute is because Emma sees in her the same capability to hurt (and kill) those close to her that she has as a young girl. However, Emma also points out one big difference, whereas she would do this willingly, X would likely have no choice in the matter due to her conditioning to a "trigger scent."
Ironically, Emma later gives one to Cyclops at the beginning of Laura's solo series, pointing out that involving her with X-Force was no different than what the Facility was using her for.
Captain America of all people gets called out on this, too: In Target: X he intends to turn Laura over to S.H.I.E.L.D. to be tried for her crimes, despite Daredevil's attempts (as her lawyer) to warn him that S.H.I.E.L.D. won't care about justice, and will only see her as a weapon to use themselves. Fortunately, Steve realizes Matt is right before he can actually go through with it.
Also X-23 and Vampire Jubilee realize they have much in common, with X-23 having to struggle with finding herself and the trigger scent and Jubilee struggling to control her newfound blood lust. They get along really well though.
X-23 also had hero-to-hero example when she joined Avengers Academy - she was afraid her Dark and Troubled Past and few mental issues it gave her will make her into an outcasts, only to learn many of the students also had problems developed by their past traumas.
And X-23 again, with her psychotic ex-handler, Kimura: Both were severely physically and emotionally abused and bullied in their formative years. But that's about where it ends, as Laura makes an ongoing effort to heal, while Kimura makes it her Freudian Excuse to inflict pain on others.
X-23 and Daken are a lot alike: Offspring of Wolverine, both raised by some very bad people, both highly-trained and dangerous killers. Despite their relationship being antagonistic, after Daken's usual bouts of double-crossings are out of the way when they first meet they actually get along and work together fairly well. When they part ways Laura is one of the very few people Daken genuinely respects, in large part because they are so alike.
Runaways also have it with The Pride, their parents.
Later there was conflict between them, and the students and faculty of Avengers Academy, full of this trope from very begining, which culminated in two groups trying to use magic to better understand each other and ending up experiencing how much they really have in common.
That he is Not So Different from his greatest enemies, especially The Joker, is repeatedly shown to be one of Batman's greatest fears. It's not an unfounded idea either; he may not be cruel or a murderer, but he's still not the sanest guy.
The Killing Joke has the Joker try to prove this to Batman in his own psychotically twisted way. In the end, after Batman proves that the Joker's biggest point, that everyone was just like him, false, he and Joker share a big metaphorical Not So Different moment, and end the book laughing maniacally together. One of the Joker's primary goals is to prove that everyone else is Not So Different from him. He tried it in The Killing Joke, and he tried it again near the end of Batman: No Man's Land when he shot Gordon's wife Sarah.
Mr. Zsasz gave Batman one of these speeches during the Knightfall crossover. His main point was that they both hunted people.
Batman himself is also regularly used as the unsavoury person from whom the hero is not so different, when other heroes accuse their Bat-raised team members.
Oracle (Barbara Gordon): while Barbara is more emotionally stable than Bruce and is actually willing to let people get close to her without being compelled to push them away, she can be every bit the manipulativeControl Freak that he is. In an early Birds of Prey storyline, Huntress called out Barbara on her secret attempts to "fix" Huntress (Huntress took issue with being considered "broken") and left the team. As she left, she accused Barbara of turning out to be a manipulative jackass just like Batman.
Nightwing (Dick Grayson): as the leader of several groups of heroes, he's occasionally being judged as becoming way too much of a drill sergeant by less, ah, obsessive heroes. Happened a couple of times in The Titans and Outsiders.
Tim Drake: more prevalent in earlier years, when Tim's Crazy-PreparedProperly Paranoid tactics hadn't come to be as accepted by his friends, and they tended to blame the fact that he could be distant, manipulative, and distrusting on Batman. Nowadays they know better.
Doesn't happen with as much regularity to the members of the Batfamily who would most rejoice in the comparison, Cassandra and Damian, both of whom want to become Batman.
Here's a weird one: In the first issue of the new Azrael, Az is on the hunt for a serial killer. During the course of his investigation, he realizes the killer is targeting people who allowed a horrible crime to happen. When they finally confront each other, the Avenging Angel gives himself the Not So Different speech, and allows the killer to depart.
In the ArchieSonic the Hedgehog comics, Scourge often brings this up to convince Sonic to be 'evil' like him. As he puts it, "All it takes is one bad day, and you'd be just like me." Throughout the series they compare themselves to one another (in one issue, Sonic says something along the lines of "My evil 'twin' conquered a planet on his own. What do you think will happen if I let loose?")
Promptly after the aforementioned Scourge quote, Sonic catches him off-guard with a counterattack, and while he's on his back, proceeds to throw the same thing right back at him, saying the real reason he hates Scourge is that if he only had a little kindness and decency, he'd be just like Sonic.
The Mist (Nash) from the 1990s Starman series gave this speech to Jack Knight, citing the fact that they were both carrying out the roles because of their fathers. Jack goes out of his way to prove her wrong by being nice to her father, the original Mist.
The Incredibles comic has this when Mirage and Elastigirl have to work together on a mission, Mirage bringing up the point that Helen ended up having to lie to her family about a new adventure as well as having been the ex-girlfriend of the supervillain they're going after.
In Blackest Night, Saint Walker tries to connect with Atrocitus by pointing out that he has lost his family as well, so he can understand his pain. However, Atrocitus retorts that Saint Walker lost his family in an accident, while Atrocitus' family was murdered.
dWARf!/Fleshmaster calls this between himself and Empowered, but she proves him wrong. Also, Sistah Spooky claims this to be true about her then-partner Mindf??k and Mindf??k's brother. (She just wanted to hurt Mindf??k.) What's really sad is that Sistah is right. Mindf??k had to psychically lobotomize herself in order to remove her less savory personality traits.
Another example occurs in volume seven, wherein Oyuki tells Ninjette just how much like her father she is:
Ninjette: If you think that I am voluntarily walking into a scenario likely to result in my death and/or dismemberment without first getting good and solidly buzzed...you are sadly f**king mistaken.
Oyuki: By sheerest f**king coincidence, this humble genin has often heard a remarkably f**king similar sentiment voiced before battle...by Kaburagi-san's own f**king father, interestingly enough.
Deconstructed in this strip◊ from Quino. For those who don't understand Spanish, it's about how a rich and a third world country woman comment on their food restrictions: While they both claim that they only eat cereals, the rich woman does so to keep her weight, while the poor woman does it because its the only thing left to eat, and they both complain of that their children eat a lot of "trash" like junk food in the rich woman's case and worms, infected water and rotten food in the third world woman's case.
In one classic Doctor Strange story, our hero finds out that the only way to defeat Shuma-Gorath is to play his own game. He puts his morals aside, descends into dark sorcery, destroys Shuma-Gorath and then kills himself before he can become another Shuma. Fortunately, his ally is able to bring him back.
Scott Pilgrim makes the realization that he's as much of an asshole as his greatest enemy, Gideon Graves. The only difference is that Scott wants to change and be a better person. This realization causes him to level up and gain a sword called The Power of Understanding which he uses to defeat Gideon.
Marvel Universe Reed Richards: So we'll begin here. With you and me. With a new focus for your ongoing and never-ending education. Our curriculum will start at survival and end at the edge of an eternal tomorrow. The rules are simple. I teach one class and it's pass or fail. Welcome to the Future Foundation.
Ultimate Marvel Reed Richards: And we'll begin here... with you and me. We're going to have a new focus for my ongoing and never-ending education. The experiment will start with survival and end on milennial tomorrow. My rules are simple. In the dome it's evolve or become extinct. Welcome children. Welcome to tomorrow. I'm sorry. Most of you are not going to make it.
Tony Stark once allowed an anti-war activist/documentarist named John Pillinger to interview him knowing the man was heavily biased against him. When Pillinger later asked him why Tony agreed to the interview, Tony responded with an Armor-Piercing Question that essentially asked if Pillinger's work has actually changed anything at all. When Pillinger admitted that he didn't know, Tony said that he didn't know if anything he has done has changed anything either. The two shake hands before parting, realizing that for all their differences they are both just trying to make the world a better place.
The majority of Hulk: Gray consisted of Bruce coming to realise that he had a surprising amount in common with his long-time enemy General Ross. Naturally, this being a Hulk comic, he didn't take it well.
Red Hood and the Outlaws: How Red Hood handles his Talon during the Night of the Owls. He relates to being killed and reanimated as a killer, and not being in control of his own life. The Talon asks Red Hood for help, as he cannot self terminate.
In My Little Pony Micro Series Issue #1 Twilight says that she can sympathies with Jade Singer having to live with extremely high expectations, since being the princess' personal students puts similarly high expectations on her.
In Transmetropolitan Spider Jerusalem has this with many people - as the story progresses all traits he shares with Yelena become more apparent, despite how different they seem at first, he quickly finds he shares the same good intentions with her father, even through socially they behave like polar opposites, and many of his rants are dangerously close to Smiler's infamous speech about hating people.