During the Busiek/Perez run, new character Triathlon wasn't held in very high esteem among the fandom. 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 CrisisJason 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 (and 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 lead to him landing right back into Scrappy dome. He still has some fans at least.
Damian Wayne, particularly since he became Robin; he is, depending on your view, either a snotty, bratty Jerk Sue who gets away with a lot of crap because he's the writer's favourite character and who should never have become Robin, or is a complete Deconstruction of the Jerk Sue who has gradually and painfully begun the process of developing from a snotty brat to a genuinely heroic character. While the character has had a sizeable portion of his haters warming up to him over the years, there are a few who won't forget his controversial introduction.
Lately, Barbara Gordon is getting heat by some fans for, to put it best, getting the silver spoon from DC editorial. Babs was for years Oracle, a beloved icon for Feminism and disabled people everywhere. Then, they made her Batgirl again, at the expense of Stephanie Brown, a fan favourite who has been screwed by DC for the last decade. Then, she replaced Steph as Nightwing in the Smallville comic. And she gets to headline the Birds Of Prey reboot as Batgirl, and appear in a few other books as Batgirl. As noted by fans, while Green Lantern fans are free to pick and chose which Lantern is their favourite and the one they want to read about, Bat fans are stuck with one Batgirl. If you're a fan of Cass or Steph, who the editorial apparently despise with a passion, you have nowhere to read them, while Babs has at least three different versions, many of which people dislike for not being as awesome as Oracle. So, she's not completely hated by all, or even hated for anything she's done, but for being the editors weapon against Steph and Cass, mostly Steph.
Which is ironic in itself, because Barbara used to be hated by DC Editorial, or at least considered a completely disposable character. They gave Alan Moore the green light to cripple her in The Killing Joke not to give her the aforementioned character development but to get rid of her altogether, and many readers/critics were disgusted at how she was treated in the book (she wasn't just shot, but mutilated and possibly raped). This was basically proven with the exact response Moore got from his editor upon double checking with him on the shooting: "Yeah, okay, cripple the bitch." It was only because two DC writers were among the outraged that she stayed in the comics at all, as they outright defied DC editorial and kept putting her in stories.
Tim Drake/Robin III got quite a lot of flack as well during the mid-late 00s period, which is odd considering he was the most beloved Robin (Dick Grayson is more popular, but many prefer him as Nightwing to Robin), due to insane levels of Wangst after his best friend, second best friend, girlfriend, dad, and step mom all died (all but the last two come back though), followed by the death of his adoptive father and being fired from the role by. Not that people don't understand, but that it came off as a heavy handed attempt at making a fun and relatable character super grim dark, and that when all these Deus Angst Machina events finished, he took it all out on others, often berating and sometimes hitting Damian (earning him hate from fans of Damian, or those who remember that Damian is a small kid), Stephanie (the girlfriend that died, who he broke up with messily and ordered to quit, earning hate from her fans), and in general, being very whiny and violent. It sizzled, for most of it, when Bruce came back and he reunited with his dead best friend and got past his anger at his ex girlfriend and stopped getting into so many arguments with Damian and in general, began acting like Tim Drake again.
Stephanie Brown herself isn't exactly popular in some circles and was openly despised for some time, with hate coming from her being the catalyst to starting off the Gotham gang war, her being less competent than the men, being a "ditz", and her rocky relationship with Tim (with her seen as being in the way of more interesting options like his old ex Arianna, or male companions). Since the reboot, she's earned more hate due to backlash from her fans' disappointment in her being erased from continuity.
Hawk and Dove:
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 Robot. 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.
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/frameup 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.
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 Connor'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).
All of the "YJ4" are considered Scrappies by diehard fans of the New Teen Titans, who accuse the characters of stealing screentime away from their old-school favorites and wishing death upon them (especially Cassie). In the reverse, some Young Justice fans consider the NTT-era members to be boring Scrappies that should get the boot. As Donna Troy and Wally West were erased by the reboot, with Bart and Cassie being kept around as the only Kid Flash and Wonder Girl, this didn't help the anti-Young Justice camp's anger.
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, previously assumed to be her revived, Terra 2, 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 also 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.
Aquagirl was also disliked by some fans, mainly people who accused her of being a homewrecker who tried to seduce Blue Beetle and get him to cheat on his girlfriend Traci 13. She also flirted with Static and Superboy, which lead to some fans calling her a slut and other derogatory names.
The DEOrphans weren't exactly Titans, but they were a group of characters that wound up taking over the late '90s run for a while, and annoyed many fans. This was due to their screentime being prioritized over the actual team, and the group being a bunch of annoying kids that felt shoehorned in to add "youth" to the series.
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.
W.I.T.C.H.: 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 beng a completely pointless character (and being made the Series Mascot despite being introduced so late.)
Another notable example is Maggot. An annoying mutant with a very disturbing power that was hyped up as being awesome amongst other complaints. Fortunately, they got rid of him after a short-but-not-short-enough ammount of time. And now he's dead.
Of course, now that he's dead, he's been posthumously elevated to Memetic Badass.
Hellion originally for being a jerkass, but has now became a Jerkass Woobie.
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.
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.
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.
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).
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 and one of the earliest-introduced Complete Monsters of the Ultimate Marvel universe; 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.
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, until World War Hulk or Secret Invasion (largely because of his interesting origins and his jaw droppingly cool fight with the Green Scar Hulk). 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.
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.
The 1994 reboot versions of Princess Projectra and Wildfire got this due to their radically different origins. 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 segregrated, with him and others living on an extra-dimensional island. His superpower was to even warp reality by screaming. Mike Grell had intentionally given him a ridiculous costume, as he hadn't liked the concept of the character.
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.