Heroic example: Otonashisuccessfully sends his friends that were in purgatory to find peace with themselves. He then tells Tenshi to stay with him in that place which pretty much while in-character, is pretty much infuriating due to the fact that their goal was to go away from that place. Thankfully, that didn't work out.
Bertolt and Reiner in Attack on Titan went through traumatic events which loved ones were eaten by Titans, yet intend to do the same thing to countless hundreds of innocent people. The motivation behind this still remains a mystery.
Berserk: Griffith admits to Princess Charlotte that the only person worthy of being his friend, is a man who chases his own personal dream, even at the expense of his own dream. After Guts overhears this, he decides to leave the Band of the Hawk after helping them win the war for Midland, to discover and chase his own dream. Griffith challenges Guts to another duel after he finds out, since at this time, Griffith has become quite obsessed with him. When Griffith loses the duel and Guts leaves, it is the point where things go From Bad to Worse, both for Griffith and for the other Hawks soon after.
Bleach's Aizen tells Ichigo to abandon his arrogance, in spite of growing more obnoxious throughout his final fight with Ichigo. Not to mention his desire to become a god; with goals like that, he really can't call anyone arrogant.
Explored in Buso Renkin. The Hero Kazuki Muto believes turning into a homunculus is wrong as the person gives up his humanity yet he later turns into a "Viktor," a enhanced human who absorbs the energy of others. Kazuki is also supposed to eliminate the Homunculi yet he is also against murdering them. He gets called out several times by The Rival and eventually Kazuki decides he doesn't care about that.
The Angels in Code:Breaker, they seem to view pretty much anyone who isn't them as evil, all while playing fun games such as "who can kill the least amount of people". Then one even states that it would be more fun to just kill them, these being the guys who believe normal people are evil for wanting to kill people.
Suzaku from Code Geass preaches non-violence and systematic change, all the while serving in the very army causing the tyranny. It's a lot worse in the second season, where his primary plan to obtain Japan's freedom is to deprive everyone else of their freedom (if necessary) just so he can get a high-enough standing to claim Japan as his own.
Ohgi believes that soldiers should not be used as pawns, which he holds to... until he uses Kallen to bait out his leader who he intends to turn over to Schneizel in exchange for Zero. Also, he contradicts his bitterness over Lelouch's disappearance during the Black Rebellion, both by his abandonment mid-season, and the aforementioned trade made without the UFN's consent that would have left its member nations abandoned.
L from Death Note, who tells Light that it is evil to murder outside the law, then proceeds to do a whole manner of illegal things to capture the 'evil' Kira, (including spying and kidnapping.) This goes to show that it is all just a matter of scale.
And of course there's Light himself. Ryuk tells him that even if he succeeds in killing all the evil people, he'll remain as the only evil person, and Light refuses to consider what he does evil.
In the 13th volume, Light considers all killings are criminal, even if they are carried out from his order.
However, he doesnt believe he should be punished for it, so he is still a hypocrite. Especially since his victims include plenty of innocent people, killed to tie up loose ends, because they were trying to stop him, or in once case when they used the Death Note to kill people for profit - even though he gave it to them and expected them to do just that.
Also Near, if Matsuda's theory that he wrote Mikami's name in the Death Note to verify it was real and prevent Mikami from doing anything that would undermine Near's plan, thus enabling him to expose Light as Kira is true.
In D.Gray-Man, the Black Order is supposed to be the good guys, and represent light to battle the noah and akuma who have darkness based powers. and then we find out about fallen ones, heresy trials, the second exorcist project, the third exorcist project, and Apocryphos.
Dragonball GT: Baby is a living DNA archive of the Tuffles, a race destroyed by the Saiyans. Baby, being the last of his kind, attacks Earth, where the remaining Saiyans are for Revenge. He establishes himself as king, recreates the Tuffle homeworld, and has just about everyone under his control. He goes on and on about how the barbaric, bloodthirsty, and cruel the Saiyans are. However, he seems to neither notice nor care that his actions make him Not So Different from the Saiyans, if not worse.
Also, according to Kimblee, Pride is this, as he insults humans and states his desire to steal Ed's body in the same breath. It's why Kimblee decides to help Ed.
Ed, Winry, and Al believe that Scar should be punished for the murders that he committed against Amestrians, but are more hesitant to believe that Mustang, Hawkeye, and the rest of the Amestrian soldiers should be punished for doing the same thing to Ishvalans. This is largely out of the belief that the latter group was Just Following Orders (and was being manipulated by the Homunculi, at that).
Scar can be considered this, as he, an Ishvalan, hates alchemy, but uses the deconstruction part of it to kill his targets. When he comes to terms with himself and realizes what he's doing is wrong, he gets a tattoo on his other arm and starts using alchemy.
Dante, the Big Bad of the 2003 anime adaptation, is also a massive hypocrite. She claims to be "above humans", just like her manga counterpart. At the end of the series, she gives Edward a big speech about how life isn't fair and that humans would destroy the world if they had the Philosopher's Stone. After her defeat, she whines about how her own efforts were ruined; moreover, she herself instigated nearly every atrocity in the past four centuries out of a desire for the Philosopher's Stone. Although she seems to believe her own bullshit to an extent, she mainly uses it as a means to excuse her colossal selfishness.
Leonard Tessarossa from Full Metal Panic!. He makes a big deal about how he's a perfect gentleman, and is shown to constantly get jealous and angry when people like Sousuke more than him, wondering why, since Sousuke is far less "cultured" and directly killed more people than him. Unfortunately, as much as he likes to think so, a gentleman he is not. No gentleman would (knowing how important it is to a woman) force a kiss on a girl who likes someone else, give the girl an Armor-Piercing Slap when she tells the other guy she loves him,just a matter of scale. or try to brainwash her so that she "won't resist him" any more (to the point where she eventually softly asks him if he "won't be violent" any more). Combining all this, there is a reason why Leonard is one of the most agreed upon Scrappies in the series.
Gundam SEED has Blue Cosmos. Their main goal is to kill all of the Coordinators, and how do they do it? By kidnapping children and conditioning them into Artificial Coordinators, which is the only way they could possibly stand a chance in 1 on 1 combat against ZAFT. It should be noted that the process used to create these "Extended", which involves drugs, mental conditioning, torture, and memory tampering is far, far more invasive than the process used to make Coordinators.
Gundam SEED Destiny: Shinn Asuka is horrified when he finds out about Stella's backstory as a Tykebomb, disobeys orders in order to save her, and is outraged when Kira Yamato cuts her down while she is rampaging through Berlin. In an earlier episode, Shinn had killed Stella's fellow Super Soldier and Tykebomb, Auel. In a later episode, he kills her other partner, Sting. In both cases, he is fully aware of who they are and what he's killing—and treats them like monsters who deserve to die.
There was also a terrorist group called La Eden, who bomb numerous cities, their reason was to stop Celestial Being from their military interventions. They state that their actions weren't evil, however their actions could hardly considered to be anything but evil, and they're just a bunch of wannabe terrorists trying to imitate Celestial Being.
The rest of the world seems to agree, as various government intelligence agencies quietly leaked the location of La Eden's home base to Celestial Being.
In Magical Girl Lyrical Nanoha A's, Admiral Gil Graham realizes that he is being a hypocrite by regretting having to seal a young orphan like Hayate away for eternity with the Book of Darkness (yet considering her ideal in a sense because few would mourn her), and providing for her until then for the sake of her happiness, which implies the belief that it would offset sacrificing her.
The villains of Master of Martial Hearts. Aya's fake friends rub it in her face that those who lost the tournament were mind raped into being sex slaves and she's to blame, despite that they were the ones who took advantage of it and cased said mind rapes. Also, they sought revenge on her for her parents causing their lives misery and grief with the original Martial Heart tournament... by bringing the tournament back.
Naruto's very own Pain tells Tsunade to not be haughty. Considering the fact that he believes himself to be a god and that he's divine... Well, arrogance is blinding, isn't it?
Then there's Naruto Uzumaki himself. He regularly chews out lecherous and otherwise perverted people, while being a bit of a Covert Pervert himself.
The dub changes his motivation, he wants to sever the link between humans and Pokemon simply because he thinks all humans treat Pokemon as tools. And of course he is using Pokemon as tools to accomplish this.
Played for laughs in the Best Wishes series: when Ash messes something up (sometimes by accident) or says something out of place, Iris would often call him a kid...even though SHE'S a kid herself! However, it's more like a sister teasing her brother than actual taunting.
The samurai from the fourth episode really gets hypocritical. He berates Ash for not finishing what he started...even though he wasn't polite by waiting for Ash to finish catching that darn Weedle. Instead, he rudely and instantly challenges him to a Pokemon battle, leaving the Weedle enough time to escape and warn its Beedrill buddies. And to top it off, he calls Ash a terrible trainer even though a Beedrill had already taken it away and he tried to call it back. Worst of all, no one calls him out on it!
Akane Tendo from Ranma ˝ says that it wouldn't be fair for Ranma and Akane to get married because she'd be emotionally crushed, but feels that it's alright for Ranma, Ukyo, and Kodachi to be emotionally crushed because it's not her.
Touga from Revolutionary Girl Utena fits this. He mistakenly believes his sister Nanami is a lesbian in the episode "Nanami's Egg" and gives her a lecture about how "evil" homosexuality is. At this point, he's sleeping with Akio
In the same episode, he also says that the reason that he and Nanami get along so well is because she's not the type of girl that lays eggs and that he pities the parents of a girl who would do that. Now, if you look at this as a metaphor for teen pregnant then it becomes clear that Touga is a hypocrite because he sleeps with so many different girls at the school and may have gotten more than one girl pregnant. Actually, it would be surprising if he managed to never knock anyone up during his high school career. So, this episode highlighted Touga's Jerkass hypocrisy.
In Spirited Away, Yubaba refuses to accept Chihiro into her bathhouse because in her words, Chihiro is a "spoiled, lazy crybaby and you have no manners". Shortly afterwards, Yubaba is interrupted by her baby, who she immediately coddles and pampers, who fits Yubaba's description of Chihiro perfectly.
Furthermore, she criticizes her employees for being greedy and attracting the wrong customer when Greed is one of Yubaba's defining characteristics.
Togainu no Chi: Akira becomes this at the end of the anime series. When he saves Rin from Shiki, he tells Rin to forget about killing Shiki because it's not worth it. Later on, Shiki kills Keisuke and Akira tries to kill him. Rin tells him the same thing. Akira doesn't listen to him at the end and returns to Toshima to kill Shiki.
Noah, the apparent Big Bad of the Virtual Nightmare Arc of the original series is the most obvious example. He mercilessly punished his minions for cheating and not following the rules, but blatantly did so himself when dueling Kaiba, using Mokuba as a human shield when he was about to lose. Yami rightfully calls him out on this.
When Yami duels Johnny Steps, Johnny plays monsters that are different types from each other. Yami calls him out on not having a real deck theme. While Yami had a point that Johnny's deck was full of cards that were chosen for being aesthetically pleasing instead of concentrating on winning, Yami had a deck with a hodgepodge of monsters as well. (This is only in the dub. In the original, Yami says he's using "fan cards" that duelists never use seriously; when Johnny uses Witch of the Black Forest - a potentially powerful card - he changes his mind and thinks he's gotten serious.)
A smaller example is Keith from the manga Yu-Gi-Oh! R. When Jonouchi uses a card called Summon Capture in their duel, Keith becomes angry, implying that the card is broken and overpowered. While most would agree that it is, Keith not only blatantly cheated in their first duel in Duelist Kingdom, but used a card called The Pillager that was a lot like Summon Capture, but probably even more broken.
Mild example, Jack Atlas from Yu-Gi-Oh! 5Ds. Even after his Heel-Face Turn, he gets very upset whenever people steal his things (even his cup ramen) or even borrow them without asking (like when Crow borrows his D-Wheel). This from a guy who previously became an outright thief in order to escape Satellite.
Mamoru Jinguji was a minor character in Yu Gi Oh Zexal (only appearing in one episode) but may have been the worst example of this Trope in the entire franchise. As the Student Council President of Heartland Academy, he was adamant about school rules being followed, but he blatant broke a lot of them himself by enforcing them, forcing Yuma into a duel with house rules that would be considered outright cheating, such as making Takashi – who he duped into working for him – force Yuma to return his monsters to his hand for dress code violations. Then it got worse. When Yuma tried to avoid breaking this “rule” by Equipping Gagaga Girl with a Spell Card that covered her, he countered it (that would be considered entrapment by any actual legal authority) then insisted Yuma be punished for “assaulting” him (meaning attacking directly, even though Mamoru did the exact same thing to Yuma just five minutes earlier). And to make this even worse, he used monsters that resembled Shinto priests to do this. (Of course, you have to forgive him for all this, seeing as he was a Brainwashed and Crazy pawn of the Barians, but it didn’t make the whole thing any less demented.)