Sam Manson, the lead female character in Danny Phantom, who is in every episode despite many of them having nothing to do with her. Creator Butch Hartman often wrote glowingly of her when he submitted episode summaries, but she is a Base Breaker in the fanbase due for her hypocritical behavior, her (for some fans) unbelievable romance arc with the titular protagonist, and the constant unbelievable talents she's given, such as being the best athlete at Casper High despite a massive aversion to physical activity. Many of the episodes on the massively panned third season dealt with Danny and Sam's relationship, to the point where even the villain was given no character development.
Midway through season 2, Drawn Together essentially became The Captain Hero Show. Practically every episode focused on him or featured him heavily, to the point where fans of other characters were sick to death of him. The writers admitted that they liked to give him stories, their justification being that the guy was so messed up that he would do absolutely anything.
Brian of Family Guy. At first he traited as the intellectual and Only Sane Man, but now this has subsided by a far lot, trying to voice his liberal opinions whenever he get the chance, and chewing people out on their religious views, most notable in "Not All Dogs Go To Heaven", where Meg converts to Christianity. It has gone to the point many fans hold a disliking to him, and further supporting fact, Word of God Has said that the character reflects his political views and serves as his Author Avatar.
Cubert from Futurama turned into a parody. He was actually created to be one of these, apparently in direct reference to the former Trope Namer, and he was originally intended to be a sort of The Ace character, except he would still be hated and mistreated by the other characters. Really only the last part became true. In his debut episode, the rest of the cast takes an instant dislike to him and manage to get in a few good insults. It helps that the writers were more in-tune than others in their profession. Originally Cubert was supposed to be the character who lampshaded all the ludicrous aspects of the series, which he does in his debut episode. However, the writers realized how terribly annoying this was and transformed him into a standard Bratty Half-PintTV Genius and only used him in a couple of episodes there after. He is also downgraded from a genius to an insufferable brat who thinks he's smarter than he is, while still acting like an actual twelve-year old.
There were so many restrictions on Disney writers to deal with Mickey Mouse, that any other character in a given Mickey cartoon practically got a carte blanche to steal the spotlight. The strange irony is that this happened because Mickey was the Creator's Pet of Mr. Disney, not the other characters.
The concept of the Creator's Pet was parodied brilliantly in Robot Chicken. It was done in a sketch featuring the producers of Star Trek: The Next Generation discussing how to make the fans love Wesley Crusher, after the fandom has paid for a billboard threatening to ass rape Wil Wheaton to death. So, they decide to include a character so annoying Wesley would look better in comparison. When one writer suggests they try to make Wesley a better character, he gets thrown out of the room. The resulting episode has an annoying Great Gazoo rip-off called "Snirkles", who proceeds to bother Wesley by playing a "space banjo song" and then disappearing. The fans then change the billboard to say "Kill Wesley. Keep Snirkles." Wil Wheaton, after seeing the sketch, tweeted that he would've loved to voice Wesley if they asked him to.
In The Simpsons, Lisa Simpson, primarily because as the rest of the cast falls into Flanderization, she remains the only consistently intelligent person in all of Springfield and gets to lecture everyone as to why her views are right and theirs are wrong with annoying frequency. By the tenth season or so, the writers seem to have picked up on how obnoxious she could be to the fans, however, and played up her hardcore activism for comedy. Matt Groening has even admitted Lisa is his favorite character on the show and he will do anything to keep her from looking bad. In Japan, however, Lisa is quite popular among viewers, so much that the show was re-marketed to make Lisa appear as the main character, rather than Homer or Bart.
Though it's not really a single character, "As Himself" is something of a taboo phrase in Simpsons fandom. Most of the time, especially post-season 10, any guest star to play themselves mostly shows up with little reason, acts cool and popular, and isn't really given anything funny to say. Hence, the star comes off as less there to service the plot, and more as a means of mooching off their popularity. Infamous examples include the stage magicians in "The Great Simpsina" and Lady Gaga in "Lisa Goes Gaga." The latter in particular received no small amount of hatred from the fanbase for being an effective Canon Sue, whose spotlight episode was massively-promoted and played very heavily on her public image without saying anything particularly new or interesting about it. Many contrasted her performance to that of Michael Jackson, who guest-starred as a fat white bricklayer living in a mental ward and received a good amount of acclaim for his part.
Princess Sally from Sonic Sat AM was a blatant example, especially during the second season, where she had as much screentime as the title character (usually at the expense of favorites such as Bunnie and Rotor, even stealing the tech abilities of the latter) and was consistently portrayed as being right all the time while Sonic was wrong, resulting in her becoming infamous as a tall order Base BreakerCanon Sue within the fandom. Dulcy was another example, getting almost as much screentime as Sonic and Sally ever since her debut. Both were stated to be personal favorites by Ben Hurst, lead writer for the majority of the second season.
Owen from Total Drama. The writers and voice actors of the show often wrote glowingly of him (Christian Potenza is quoted as having a man-crush on him), yet he is reviled by the fanbase due to his constant Toilet Humor, Character Shilling (such as Gwen calling him sane even when he does exceedingly odd things, and the rest of the cast talking about how awesome he was during his elimination in the 2nd season, despite the fact that he cost the team the challenge and spent the entire episode trying to eat two of his teammates), and Character Focus (such as extended dream sequences of him naked and frolicking on mountains made of cheese). His face was even used as the icon for the first season on at least Cartoon Network. However, the third season changed this, as Owen received much less praise from the other contestants, and he received some decent character development with his friendship with Noah and his breakup with Izzy. The writers must have noticed the backlash, as Owen does not appear in Seasons 4 and 5, save for minor cameoes.
Mike and Zoey, especially once All-Stars aired. While Mike was more tolerated by fans for at least having a story arc (at least until the reset button reared its ugly head), Zoey was just a plain, normal girl that the writers tried to promote as an ultimate heroine and embodiment of goodness.