During the Busiek/Perez run, new character Triathlon wasn't held in very high esteem among the fandom. Some of this was due to being a member of a Church of Happyology, some of this was due to his being foisted on the team by politics, but mostly due to his acting like a Jerk Ass to the established characters people actually like. After he left the group, any enmity against him was largely forgotten - until he mercilessly killed Crusader at the end of Secret Invasion.
Wonder Man earned this reputation back in the 80's, when he was a member of the West Coast Avengers. The fan reaction to the infamous storyline where he tried to break up Scarlet Witch and the Vision so that he could date the former earned him the ire of a number of readers.
Post-Crisis Jason Todd was hated by quite a few readers, to the point that fans eventually voted for him to be killed by the Joker. While an almost equal number of people voted to spare him (it is rumoured that at least three hundred of the votes were from the same caller), a LOT of people thought that the vote was for the first Robin, Dick Grayson, who was excessively popular amongst a lot of fans.
Funnily enough, he was brought back to life due to Alas, Poor Scrappy status, where he became an anti-hero Jerk Ass Woobie who was centre stage to a very well received storyline. However, poor use led to him landing right back into Scrappydom. He still has some fans at least.
The Riddler. Not as bad as most others, but is generally labelled as the lamest of the big name rogues, with a mental disorder (OCD) that many find dull in comparison to the others. Emphasizing him as a "technically legal" villain has since quieted some of them down. Though back in the Golden Age and Silver Age, he actually was one of the most popular villains, mainly from Frank Gorshin's manic portrayal on the 1960s Batman TV Show.
Pretty much all of the new characters introduced in DC's Bloodlines crossover during the 90s count with a few noticeable exceptions including Hitman by Garth Ennis and Anima, whose series lasted fifteen issues and was nominated for two different Squiddy awards. Basically most of the New Blood characters were walking epitomes of the excessively Darker and Edgier 90s with such names as Ballistic, Nightblade, Cardinal Sin, Jamm, and Mongrel. All of them gained powers when they were attacked by alien parasites who feed on spinal fluid and were based after the Seven Deadly Sins. Even in-universe the New Bloods are looked upon with disdain, with such heroes as Kyle Rayner and Wally West mentioning that they were nothing but a bunch of incompetent hero fan boys who ended up dead a year after their debut. Though there are certain people who feel they have some value and argue that they were a product of the times.
Holly Granger, the female Hawk. It doesn't help that the original Hawk (Hank Hall) was changed into a villain with Armageddon 2001 thanks to an Ass Pull when Captain Atom was leaked as Monarch and DC wanted to keep things a "surprise". Then come 2005, after Dawn Granger/Dove II's death was undone with a convoluted and squicky explanation: Dawn, an only child in the Hawk and Dove series, suddenly shows up to the Titans with a bratty younger (or older?) sister in tow that was living away in England all the while. Fans of Hank Hall immediately cried foul on Holly, for not only did she have an inconsistent and unlikeable personality, but her existence also retconned the fact that Hank and Dawn's powers were bound to them and could NOT be passed on to anyone else. It wasn't uncommon to see those fans wishing death on her and wanting Hank back with an Author's Saving Throw, in the end they got their wish with Blackest Night.
Before Holly and long before Dawn's comeback, DC attempted to do a completely different take on Hawk and Dove, with an army brat named Sasha Martens and a slacker musician named Wiley Wolverman gaining the power to sprout bird wings and fly, as well as telepathy. Due to them being a case of In Name Only and not being received very well by H&D fans, these two wound up vanishing with no explanation given, not even showing up as cannon fodder for big events. Would it have helped if the artist had known how to draw bird wings that don't appear to be suffering from both crippling arthritis and mange? Guess not...
Judge Dredd: Walter the Wobot. He was fine, until they decided to give him a speech impediment. Do you have any idea how many 'r's are used in the average English sentence? You will after reading his dialogue, as every single one turns into a 'w' that drills into your soul like a misshapen bullet. And of course, he worships Judge Dredd. And for some reason Dredd puts up with it! Walter eventually gets his own feature.
In the Justice Society of America, the character Magog is hated by a lot, partially because he's a massive Jerk Ass who got a lot of time on screen. A LOT of people also cite him hittingMaxine'Cyclone'Hunkel when she was flying overhead because 'she came at him from his blindspot.' Magog has also been accused of being a mouthpiece for writer Bill Willingham's right-wing views; fans were quick to call Unfortunate Implications when Magog took center stage in an arc that also featured Obsidian (who is gay) being turned into an egg and Mister Terrific (who is black and atheist) being shanked in the back like a street thug (both eventually got better).
Big Daddy from Kick-Ass, for basically turning his daughter into a killer just because he was bored with his life.
Lori Morning wasn't very liked by fans, as she was a bratty Tagalong Kid that lacked powers, only being able to use her H-dial to morph into random superheroes. The fact that the creative team intended to be a younger version of the villainess Glorith didn't help matters. Putting her on a bus was one of the first things to occur once a new creative team took over.
The 1994 reboot versions of Princess Projectra and Wildfire got this due to their radically different origins. Projectra went from being a princess to a giant talking snake, while Wildfire became the result of a Fusion Dance between two minor supporting characters. The later never recovered though the former did garner a level of popularity.
Tyroc, the first black character to join the Legion, combined this with some Unfortunate Implications: He was an angry black man-type character whose backstory implied that the 30th century was actually that racially segregated, with him and others living on an extra-dimensional island. His superpower was to warp reality by screaming. Mike Grell had intentionally given him a ridiculous costume, as he hadn't liked the concept of the character. After the original Legion continuity became prominent once again, Tyroc was returned to the team, with his controversial origin never mentioned and a less ridiculous new costume, to the relief of many.
None of the Marvel Scrappies above, however, compare with reporter Sally "YouTube is more important than personal liberties" Floyd. Yes, she actually expressed that viewpoint, and what's more Word of God says the reader was supposed to agree with it. There is even a list for the Top Ten Reasons to hate Sally Floyd◊. Paul Jenkins seems to have a flair for creating these, actually, as he's also coughed up the ridiculous and biology-defyingSpider-Man villain The Queen (later Rescued from the Scrappy Heap by Dan Slott) and everyone's favorite Invincible Hero, The Sentry (though, to be fair, the Scrappification of this character only came into full when other writers began using him; Jenkins has nobody to blame but himself for the disastrous Fallen Sun, however).
The Sentry was originally well received (largely because of his interesting origins and his jaw droppingly cool fight with the Green Scar Hulk), until World War Hulk or Secret Invasion. Unfortunately, Bendis got hold of him and turned him into Norman Osborn's pet killing machine with the mentality of a child, and gave him more powers than Silver Age Superman. This, combined with the fact that writers kept changing Sentry's origin and his relationship to the Void (The Void is Sentry's split personality! The Void is the real Bob Reynolds, who was a druggie! The Void is the Angel of Death!), meant that eventually every reader had stopped caring about who the Sentry really was and just wanted him to go away.
Drago Wolf, the Wolf Pack Freedom Fighter traitor. No one likes the misogynistic bastard, not even current writer Ian Flynn (who has gleefully stated he only brings the guy out whenever he wants him thrashed by the good guys). The fact that he's a despicable coward whose only claim to fame was tricking his former girlfriend into playing the patsy to a murder/frame-up in a totally illogical and scientifically impossible way, and joining an anti-Freedom Fighter team that he's contributed nothing to, during his tenure there doesn't help his cause, any.
There's also Tommy Turtle. He was originally a one-shot character that revealed that he had given Sonic a life lesson when he was younger and had performed a Heroic Sacrifice to save Sonic from an ambush. However, he ended up returning after a Time Skip, healthy, whole... and attempting to replace Tails and Rotor. When Ian Flynn took over, he compiled a list of characters in the series and arranged them in popularity, finding out that Tommy was STILL at the bottom. He's promptly killed off during Ian's collection of Author's Saving Throw.
None of these are a patch on Michelle Gonzales, a token love interest for Peter from the BND era. Michelle is a violent bully who wound up becoming Peter's roommate when Vin went to prison, and regularly insults, abuses, and humiliates Peter.
Carlie Cooper's increasingly Purity Sue-like portrayal is resulting in a massive backlash from fans. Originally it was more along the lines of Replacement Scrappy for MJ, but it escalated when everyone, from past girlfriends to best friends, kept telling Peter how 'right' she was for him because she's his 'intellectual equal'. It was REALLY not helped by the fact she would get mad at Peter for the stupidest things, was pushed as a Woobie because her hero cop dad supposedly died only to be revealed he wasn't a hero and wasn't dead, act like a hypocrite, amongst other problems. She's also received ire for having similar characteristics as four of Peter's past love interests: troubles with father (MJ), Nerds Are Sexy and attempted Adorkable (Deb Whitman), loves Peter for him (MJ, and an invert of Black Cat), is old friends with Harry Osborn, a tsundere, and Peter's 'true love' and perfect girl (Gwen). You could make the case that the writers are trying to evoke Gwen Stacy in her character, but in the end comes off as a lot like Lana Lang in Smallville and the equally hated film version of Mary Jane. In the aftermath of Spider-Island, she was demoted to a supporting cast member without romantic interest in Peter.
Carnage has been around for quite some time, and while he does have his fans, a sizable chunk of the fanbase really hates him and always has hated him. When he first came out, he was widely decried as a Joker copy minus any of what actually made the Joker a good villain. His near-total lack of meaningful character development has not helped his cause one bit; being a violent nihilist who devotes his entire existence to murdering as many people as possible just because he can may have worked just fine in the Nineties, but as comics began to move away from that type of thing, he did not change one bit. His tendency to go around inflicting The Worf Effect just to show how much of a threat he is in spite of it having been well-established also doesn't tend to go over well. Marvel at least seems to be somewhat aware of how widely disliked he is and periodically does things to try and re-establish him, but none of those attempts have ever actually addressed the core issues of why fans hate him.
Superboy-Prime since his Face-Heel Turn in Infinite Crisis, mainly because he became DC's Straw Fan, mouthing common fan complaints while committing villainous acts. Although most of his most infamous moments were rendered non-canon (no one got out of Countdown to Final Crisis unscathed), people still haven't forgotten them OR the stuff that is canon.
Danny Chase. Not only did he actually look like Cousin Oliver, but everyone hated him. He mocked Jason Todd's death (in front of Dick Grayson, Jason's adopted brother) and his sole Crowning Moment of Anything was his own death.
Pantha and Baby Wildebeest had received hate and ridicule for being "awful '90s characters" from various fans, although their deaths in Infinite Crisis showed them to be more on the Base Breaker side, as many other fans decried their horrible fate.
Flamebird. After the first Crisis, the original Bat-Girl no longer existed and Barbara Gordon was deemed to be the original. When Marv Wolfman and George Perez decided to revamp the Titans West team for the Post-Crisis origins of the Teen Titans, Betty Kane was reintroduced as Mary Elizabeth ("Bette") Kane, now with the codename Flamebird and a Valley Girl with a strong desire to get the affections and praise of Nightwing in any way. As Wolfman had no love for the Titans West save for Lilith and Changeling, the portrayals of the revamped versions, ESPECIALLY Bette, earned them spots high on the Titans "Scrappy" list. Flamebird wound up as a Butt Monkey-type character for years to come, even though some writers attempted to make her seem more interesting through "depths" in her origin (stating her physical prowess and skills that rarely seemed to be reflected). Geoff Johns started a more streamlined take on the character in the Beast Boy mini-series, and it seemed that Greg Rucka was attempting to revise her into a much more competent heroine. The New52 pressed the Reset Button via the Batwoman series, as Bette now lost most of her established history (and previous upgrade), making her come off nearly Too Stupid To Live and get mutilated by an enemy. She's later appeared to have gone back on track to a darker and more serious revamp in her costume, but time will tell if this change is successful.
Golden Eagle was initially hated for being a shoe-horned attempt to give Hawkman a sidekick and knockoff in the Pre-Crisis era, and was hated Post-Crisis for being a slacker surfer-type guy who'd only fight if it could get him women and attention. He got a little sympathy after being killed off, but after Jimmy Palmiotti and Justin Gray retconned his death and revealed him to be a Jerkass-type villain with a grudge against Hawkman, fans had new reason to despise the guy (or the direction he was taken in).
Cassandra Sandsmark, the current Wonder Girl; it didn't help that Cassie was mostly pushed as a Purity Sue ŗ la Donna Troy by writers, when in truth she came off like a raging Alpha Bitch after her boyfriend's death. Itís worse when you remember that she started out as her schoolís lovable geek. Her New 52 version has similar controversy, but is also hated for being a thief, being "overtly sexualized" and having her connection with Wonder Woman only recognizeable to readers of Wondie's book (she's the daughter of Diana's half-brother, i.e. the niece of Wonder Woman, though neither of them know about it as of now).
Once Conner returned to the series (before the reboot), you think she wouldn't have had much reason to keep lashing out at her teammates, but some writers felt differently. Under Johns' (ironically) and others' pens since Conner's return, she had been portrayed positively and having gotten over her grief. But other writers, especially in the case of Felicia Henderson, had continued to portray her as an angry shrew, who even goes as far as to treat her back-from-the-dead boyfriend like crap (eventually leading to their breakup).
Tara Markov, Terra of course, isn't exactly a well-liked character. She was the original comic's mole, and a Psycho for Hire who toyed with people's emotions and taunted her former friends.
Her doppelganger Terra II, was more liked, although some fans of the Beast Boy/Raven ship threw potshots at her (until her death). Atlee, the third Terra, managed to become something of a fan favorite due to her supporting role in the Power Girl series.
Prysm, a member of Dan Jurgens' volume 2 team, isn't very liked by some classic fans due to coming off too naive and stereotypically feminine, spoiled, and her visual appeal mostly coming from the fact that she was nude all the time.
Fringe from the above run is also hated, for lacking personality and never being as developed. Unlike Prysm, it's hard to find fans that can tolerate him.
Minion from Wolfman's New Titans is either hated or ignored by most fans due to the fact that he came in during a Dork Age, and that he seemed to be pushed in as a cool new teenage character but lacked interesting traits.
Bombshell was widely disliked by a number of fans during her brief tenure on the team. She was criticized for having very little personality and was accused of trying to ape the characterization of the recently departed fan favorite Ravager. The fact that she was a Motor Mouth and a Jerk Ass didn't do much to help her standing with fans.
The DEOrphans, a group of metahuman kids from the DEO, were hated even more than the unpopular Titans. This was because they got in the way of the Titans' screentime and that they were simply useless at fighting or doing much to advance the plot. Their presence also caused the "Epsilon" arc to be heavily rewritten, and a bunch of other planned stories had been thrown out.
Terry Long, for being considerably older than Donna, coming off as creepy, and his tendency to make blatant passes at her friends. He actually became even more of a Jerk Ass in the '90s, before he was killed off in John Byrne's run of Wonder Woman.
The rest of the Team Titans besides Terra II. While they've come to have some nostalgic fans in recent years, the general Titans fanbase widely loathed them and still looks down upon them, as they were a publicity stunt used to shake up the book and came along with other plot twists that ran the title into the ground. The common criticism is that the characters relied on dated '90s and Twenty Minutes into the Future stereotypes. Out of the group, Mirage is most criticized for committing rape by fraud (in disguising herself as Starfire and tricking Nightwing into having sex with her). The later writer of the "Team Titans" title had even wanted to kill off Mirage due to her unpopularity, but this was averted. Killowat and Prestor Jon also became loathed, both for becoming increasingly assholish to their teammates and especially because of the ignorant racist comments that the former made about Mirage being "pretty for a dark skinned girl".
Deathstroke's Titans team qualifies for this status as well. They are even more so ignored than Fringe and Minion, who are at least mentioned in nostalgic regard when discussing the past Titans team, whereas Slade's team of mercenaries is completely ignored save for when someone is mentioning a member that was already a Titan (Roy, Osiris) or associated with the group (Cheshire, Deathstroke). Most fans wish to pretend Eric Wallace's run on the book didn't exist because of the extreme levels of gore, stilted dialog, Roy Harper's ongoing Character Derailment, and the book's starting point being Ryan Choi's prolonged murder. Even a gracious creator like Gail Simone couldn't defend the Villains for Hire special that started this run, and she almost never badmouths any comic.
The Ongoing gave us Spike Witwicky. Humans are always hated by fans, because they're humans (and judgement is often too harsh), but not Spike, he's a huge Smug Snake. He's killed, or threatened to kill Transformers. He neglects his commanding duties in favor of one-night stands, or personal grudges. He's also been Evil All Along, and he has been working with the Swindle to get technology and kill all cybertronians. This means he's probably one of the few intentional scrappies.
Ultimate Marvel has their take on Deadpool, primarily amongst fans who had come in from the original Marvel Universe. 616 Deadpool, while having originally been created as basically a rip-off of Teen Titans villain Deathstroke the Terminator, is well-known in current pop-culture for going so deep into Chaotic Stupid that he emerges in the deepest part of Chaotic Awesome, glorifying in surreal, bloody-yet-whacky antics and lots and lots of fourth wall breaking, perhaps being the best known comic version of the Fourth Wall Observer. 1610 Deadpool, on the other hand, is a horrifically mutilated cyborg; not only is he an active participant in a mutant-phobic country's sick program of kidnapping mutants from other countries and then hunting them down to slaughter them on national live television for entertainment, he's fully aware that they are usually innocent. He just hunts them anyway because he finds it fun. In other words, Ultimate Deadpool is crazy, but in a sick and horrifying way, whereas Mainstream Deadpool is pure Crazy Awesome, and so the fans of the original revile the Ultimate version — the closest Ultimate Deadpool has come to being Rescued from the Scrappy Heap is when he appeared as a Composite Character (Ultimate Marvel appearance, Marvel Comics personality) in Spider-Man: Shattered Dimensions.
From The Walking Dead comic, there's Lori. Abandoning her husband without even a note, cheating with his best friend less than a month later, confronting a very angry farmer, confronting potentially violent inmates, being completely worthless in battle, having no other abilities whatsoever, and never bringing anything to the table other than bitch and whine, she's even more of a Scrappy when compared to the far cooler and tougher Michonne or Andrea.
In the comics, Orube took flak for a while, some of it perhaps because of fears that traditionally, new additions to longtime Five-Man Band stories tend to be bad ones. Most of the hate died down eventually though.
We is also widely hated, mostly due to being a completely pointless character (and being made the Series Mascot despite being introduced so late.)
Another notable example is Maggott. An mutant with a very disturbing power and a thoroughly annoying slang that was hyped up as being awesome amongst other complaints. Fortunately, they got rid of him after a short-but-not-short-enough amount of time. And now he's dead.
The third man to go by "Thunderbird", Neal Shaara, by virtue of having absolutely no right or reason to use that name; the original Thunderbird and his brother were both Native Americans with superhuman strength, durability, and speed. Neal is/was an Indian with fire/energy powers. Having the popular Psylocke dump the also well-liked Archangel for this guy also rubbed people the wrong way.
Moreso than practically any other teen X-Men character, Ink from the very short-lived Young X-Men series was hated by many fans. The fact that the writer went to extreme lengths (like ya know, giving him the power of Phoenix) to make him seem important did not go over well with fans, and he also had the stigma of being a human rather than a mutant. Being a Jerk Ass and bizarrely ending up with Emma Frost in a Bad Future also didn't help.
Icarus already had two strikes against him, having been created by the fan-reviled Chuck Austen and introduced in what's generally considered one of the worst X-Men stories of all time. His Wangst didn't so much tip him over the edge as throw him bodily off of it.
Very difficult to believe now, but Kitty Pryde started out like this. Her introductory story was fine, but it quickly became obvious that Claremont had no idea what to do with her after John Byrne left. He finally appeared to get a handle on her character in the Brood arc (which also introduced Lockheed, her constant companion) and the story "Professor Xavier Is A Jerk!" which was fittingly about Kitty Pryde justifying her membership in the X-Men.
The Scarlet Witch is a massive one. While Avengers fans have her as a Base Breaker for killing some of their members and disbanding the team, she was eventually forgiven, and she had gone through a lot. To X-Men fans however, she single-handedly sent them into what some view as a big Dork Age and basically almost wiped out her own people. She literally depowered the vast majority of the mutant race, leaving only an estimated 200 mutants left in the world. The brutal depowering is actually shown. Then, when she returns, the Avengers prevent the X-Men from making her pay for her crimes. Many perceived her treatment by the Avengers as Easily Forgiven, especially since what she did to them had been pretty much fixed, while the X-Men were still struggling to survive. Then, she acts all self-righteous to Cyclops (who, by that point had become a big Ensemble Dark Horse due to writers' attempts to get readers to dislike the guy failing miserably) concerning his actions to keep his species from going extinct, which, let us not forget, were directly her fault. In short, when a character nearly commits genocide on a race that is central to a series, she will not be well-liked by fans of that series.
Young Justice: Slobo/Lil' Lobo was a polarizing figure among fans and writers. The final issue of the series saw him transformed turned into a living statue and he has not been seen or mentioned since. DC editor-in-chief Dan DiDio reportedly despised the character, and claimed that he nearly ruined the original Lobo.