In Winter War, Urahara notes that he and Mayuri are really very similar in their desire for knowledge for its own sake, and that the only thing that keeps him from performing Mayuri's experiments is that, unlike Mayuri, he likes people and wants them to like him back.
A Protector's Pride has Byakuya say this about Ichigo and Yamamoto despite their dislike of each other. Both will fight viciously for their beliefs, goals and True Companions. Byakuya however notes that this must hurt Yamamoto more since Ichigo might remind him of his younger self but years of compromise and dealing with the (corrupt and xenophobic) Central 46 made him Lawful Stupid whereas Ichigo didn't cave in despite Yamamoto acting like a Obstructive Bureaucrat to him.
Also, he tries this with Monkey Khan since they have a need for revenge.
In Connecting The Dots Hinata finds a kindred spirit in Lois Lane while Lois describes Superman in a way Hinata finds familiar. Readers also get to see that Superman and Naruto are also not that different during Lois' description of Superman.
Lois: "He just has...something inside him that compels him to help people."
Mare of Steel: Trixie tries pulling this on Rainbow Dash when they run into each other in Seaddle, saying they're both arrogant braggarts. Rainbow Dash shoots this down.
Princess of Themyscira: Ares says this about himself and Athena, pointing out how they both manipulate the mortal realm to their own ends.
In Kyon: Big Damn Hero Kyon realizes this and mentions it to Wataru as both want to protect their loved ones, in particular each one's sister.
Lecture for Moo Moo has Woody admitting to Moo Moo that she is going to a similar case to Lotso as both of them are abandoned by their owner by accident, not going back to them, and they're oblivious to the fact that they're the abandoners, not their respective owners. He successfully convinces her not to become like Lotso.
Renamon Who has Valmont admitting to Rika they're so alike. Both of them are rich, have a spoiledattitude. That second statement reminded him when he was once a kid and still has it as an adult. Neither of them treat their non-human partners right; as a result, they lose them. As much as Rika said she doesn't need Renamon and that she hates Digimon, Valmont shares those same feeling with Shendu. When Rika tries to deny those, she eventually realizes Valmont is right; she has become like him.
In When There Was A TomorrowShepard and his crew can't help but see an uncomfortable number of parallels between The Illusive Man and Dr. Halsey, and several of his teammates seem to be losing respect for him for siding with her, maintaining loyalty only because Shepard thinks she's their only ticket home.
In Depravare Kira and Righteous (Light and L) have always readily accepted this about each other and are offended when Near doesn't get it, he doesn't want to see Kira as anything but an evil mass murderer and his mentor as anything less than a saint.
"You make me sick. Both of you. You're just like him. You call yourself justice...but all I see i-is a monster, a-a pathetic hypocritical brat who makes up whatever sounds good at the time so you always have an excuse to do whatever you want. You made that abundantly clear when we were messing with Yotsuba; I just made the mistake of thinking that you could move past that. This wasn't about saving anybody, this was just about satiating your fucking egos. I don't care if you're the world's greatest detective and I don't care if you've got your own goddamn screensaver; to me you're just one of the stupidest most over-glorified self-entitled bastards I'll ever meet! You and him! Fucking stupid bastards!"
In the Uplifted series, it is an overall theme of the stories. To the average grunt, the World War II wasn't that different irregardless of who you fought for, as seen during the Invasion of Malta with Rommel's troops. Seen particularly in Skorzeny and Churchill.
When Celestia and Discord meet each other again for the first time in Act II of the Legends of Equestria continuity, it's because Celestia is summoning Discord's magic to make herself more powerful. Moreover, Discord reveals to her that he was once a unicorn like her, before he accepted dark magic as a way to get his life back.
In Act IV, Discord reveals that he is in fact Celestia's great-great-great-grandfather.
Rainbooms and Royalty: Just before the Final Battle, as part of her pitch, Nightmare Moon pulls this on Rainbow Dash, saying that she knows what it's like to have one's self and achievements overlooked in favor of another. Dash, however, doesn't buy it.
In All-American Girl, despite being raised as a human and not a pony, DJ clearly shares a temper and obstinacy with her biological mother Rarity that is all too-well noted by just about everyone/everypony who knows either of them.
Hit and Hug has Rainbow Dash admitting that she's not too different from Fluttershy since both of them are arrogant and realize the error of their ways to make amends with their friends.
The rather odd Team Gai (Naruto, Hinata, Lee) from Geniuses of Hard Work puts three Determinator's who are considered weak for being differenr with two being considered "dead-last".
The reason why the team of Hinata, Naruto and Shino from Team8 is so popular. All three are discriminated/hated/mistreated in some form which leads to a rather close-knit team.
In the oneshot Story Like Me found here http://www.fanfiction.net/s/9092514/1/Like-Me, it is Orochimaru who tells Sakura and others that Naruto is more like him than anyone could think of. People scoff it off at first but as he goes on into details, it becomes startling clear that Naruto is similar to him.
In the last scene of The Second Try, Shinji admits he finally understands his father a bit, since when he thought Asuka was dead he almost started the Instrumentality right on the spot. And he would have done if Asuka would have not reached him in time.
Kaworu taunts Asuka stating maybe she knows him better than she admits.
"Oh, but it's true. Face it, moron core, you are nothing but a cold, heartless, sadistic, unloving machine. Just like me. You may look human. You may sound human. You may act human. But that's only because I wanted to see how long a robot could live a lie. You're more like Hal than you want to admit. You're more like me than you want to a-"
In Tengen Toppa Gurren Solvernia, Nia undergoes through a small Heroic BSOD in the beginning, after realizing that the beastmen are people just like she and other humans are. It's part of her inner conflict to protect herself and her friends and trying to make peace with the beastmen.
Nia: I don't understand... if they're like us, then they wouldn't have any reason to hate us, would they?
In the fanfic Camp Scare Abby realises, due to her traumatic childhood, she's Not So Different from the children she was being a Jerk Ass to.