Xykon on his good days. In the author's own words, he's not just evil, he's also kind of a dick.
Both Thief and Black Mage from 8-Bit Theater. Sarda also fits, since he's an omnipotent chaotic Trickster Mentor (an example is when he threw Australia on Black Mage, not only to punish him for being disobedient but also because the resulting wave would destroy the city White Mage was helping reconstruct).
Thief is a more intellectual type of jerkass mainly motivated by greed and feelings of elven superiority, who loves screwing people over with legal contracts and l33t ninja skills. Black Mage is, by all accounts, a smelly sociopathic fat little creep with horrible manners vis-a-vis women, to the extend that (it is said) the universe exists to hurt Black Mage. On the other hand many people would love to kick Thief in the groin face, but ever since he upgraded his class to ninja, he's (nearly) impossible to hit.
Mike from Shortpacked!, although he knows he's a jerk and makes a conscious effort to make everyone else miserable. He gets to keep his job at the store because he sells the most product insurance plans by outright threatening people.
Most of the cast of Something Positive. Davan likes to go up to random children and convince them their parents want to kill them, Jason enjoys trapping people into excuses to berate them, Aubrey and Peejee consider assaults on strangers and loved ones to be massively good fun. Kharisma, on the other hand, is currently serving time for a murder she didn't commit ... but was bragging that she was going to. And yet someone is trying to make a movie out of it. Mike started out this way, but he became more human and likeable throughout; at present, he's about the most sympathetic member of the main cast. Most of the cast claim to become sexually aroused by the suffering of others. At this point in his development, Mike is close to being the nicest guy in the strip, and there are times Kharisma comes off more sympathetic than the main cast; at least she's suffering for her sins. Mike seems to have realized what a bastard he was, and has decided that he needs to grow up and mature. He's the only person to actually make such a decision, with the rest of the main cast staying horrible, horrible people.
The above notwithstanding, most readers actually like him, not just the author. Every evaluation above could be heavily questioned, though Squishydodo (the one whose son is now called "Squishybunbunbunbun") indeed seems to suffer from Stockholm Syndrome.
Reynardine from Gunnerkrigg Court is... difficult to categorize. His introduction to the story involved him attempting to kill Antimony, an act he has yet to show any remorse over. Since then, he appears to be undergoing a drawn-out Heel-Face Turn, but it's unclear how much of it is really him and how much is just his Restraining Bolt. Rey is, in turn, surly and pleasant, disruptive and helpful, lewd and respectful towards his owner. (For her part, Antimony mainly keeps his company so she can prevent him from doing any real harm, and because she wants to know how he knew her mum.)
The Hat Guy from xkcd is a good example, asshownbythesestrips (given that he's an Expy of Aram). The Hat Guy's new girlfriend/archenemy also follows this trope.
As the Secretary arc proved, he has a long history of assholery. Proves he's something of a Jackass of all trades.
Dominic, from UG Madness. He has a rival, Permission Sam, who's possibly even more of a Jerkass.
Despite the original intention of his being a straight-man, Pennsylvania GovernorDoctorZexion Doreone of Ansem Retort has grown to be the comic's most prominent Jerkass in a comic full of them. He's helped hijack a plane, embezzled tax payer money on hookers, planted explosives in his patients and generally ruined the lives of most everyone around him. The only person that seems to enjoy Zexion's company is Axel, a psychotic mass murderer (who saved Zexion from impeachment by Phoenix Wright by threatening the judge and jury ... after killing three previous juries).
Axel and Darth Maul. Yes, THAT Darth Maul. Namine and Aerith help Zexion in his administration though.
Cassiel is willing to beat an innocent party goer over the head and strip her naked to get into a party to make life difficult for Ash and destroy Rumisiel. Maybe it's that her uncle is Lucifer that makes her act that way or maybe it's because no one will let her forget it.
Sheldon is an egotistical, arrogant and manipulative jerk who abuses his old friends' trust, even stating outright that they're just 'dumb muscle'. He also seems out to claim as much influence as a driver as possible, kicking people off their own roads in racing gambles and using his muscle to ensure they stay off. Also doesn't take kindly to losing a race/bet—when Ash beats him, he smashes his own car up with a rock to make it look like he was on the receiving end of cheating. Fortunately, he's given a Humiliation Conga he won't soon forget.
Heather has made it her mission in life to destroy Ash because her crush liked Ash better. So far she has failed miserably in all her attempts, which usually amount to beating Ash by proxy.
Topato Potato from Wigu, who lives in a dimension whose survival depends on how much Magical Adventures in Space merchandise Wigu Tinkle purchases, and is willing to do anything, from beating his father to blowing up entire timelines to keep Wigu interested and buying. He would likely be even more of a Jerkass if his partner, Sheriff Pony, didn't serve as his conscience, if not a particularly successful one.
Rayne from Least I Could Do most certainly qualifies. Self-centered, self-absorbed and prone to assholery at the drop of a hat for his own amusement. He frequently crosses over into Jerk with a Heart of Gold territory.
Sonya, the subject of some of Zii's early thoughtlessness, can be seen as Zii's actions having incarnate consequences. Her Serious Business approach to seduction can make her as bad as Zii, for whom she becomes a Stalker with a Crush (taking the role over from Yuki), and she can be really petty and bitchy at times — sexting Gary while he's on a date with Kiley, putting Gary's hands on her breasts to purposely unleash Yuki's fury on him so she can make a move on Zii, pulling similar moves on Gary to purposely provoke Yuki, gloating over Zii's break-up with Erik... She manages flashes of kindness, though; her worst features mostly derive from her obsession with Zii.
The initially sweet DiDi's obsessive search for an orgasm, probably from Gary, sent her across the line a few times; trying to break up with Matt by text message, trying to undermine Kiley, and taking every opportunity to get seductively naked with Gary, for example.
On the male side, we have Jordan, who basically mindscrewed Gary into confusion about his own sexuality, Matt, who at least admits he's a bastard, Dillon, whose own obsession with Gary soon gets out of hand, and the just plain obnoxious minor characters Nathan and Takeru.
Girls with Slingshots has many jerkasses in its cast, but the absolute queen of them all is Candy, who early on attempts to rape Chris and refuses to forgive him for daring to resist and escape, goes out of her way to sabotage her supposed best friend Jameson's relationship with his girlfriend Maureen because she's in love with him herself, and eventually becomes a professional dominatrix, which is probably the least jerky thing she's done. Her hatred for Maureen culminates in her attempting to sabotage her wedding to Jameson. It backfires. Gloriously.
Toadsuke from Supah Nario Bros crosses into Jerkass territory from time to time.
AG: Apologiiiiiiiize!!!!!!!! AG: Say you're sorry for being a cripple! Wheeeeeeee! AG: Aaaaaaaahahahahahahahaha!
Eridan is quite the Jerkass- not only is he hugely self-obsessed and just generally obnoxious, but he is also a strong proponent of killing all the lowbloods. Which he eventually partially succeeds at doing.
Kankri, Karkat's ancestor, is a very subtle kind of jerk. He constantly avoids triggering or insulting people directly, but he does so in such a condescending and faux-intellectual manner that he winds up insulting them anyway. He's a bit of a hypocrite too.
Cronus. It says a whole lot that he is creepier than Eridan.
Meenah, although it's been shown that she is not the worst member of her group and does have Even Evil Has Standards moments.
Then there's Caliborn, who's kind of a sadistic prick even at the best of times.
In Soul Symphony, Charlie's rants about how his bitter rival, Tom Mustaine, is one. He even wears sunglasses indoors.
Elf Blood has Gipsy, a human sorceress who generally treats everyone like crap unless they hold some sort of authority over her.
Si-Hoo from Orange Marmalade, who repeatedly likes to torment Ma-ri (having said multiple times that he would out her vampirism to the entire school). When Ma-ri had her pig-blood-bag stolen by Ah-ra, he gives her a real one and laughs over her while she's trying not to be sick. While he does force Ah-ra not to out Ma-ri as a vampire it's clear he does this to protect himself.
Dillon, the title character of Sticky Dilly Buns, is probably meant to be cutely camp and whimsical, but shifts into jerkass territory with some readers for his casually manipulative attitude towards Ruby, his possessiveness towards Jerzy (which doesn't stop him from flirting with every other cute man in sight), and the tricks he uses to press his body up against clueless straight guy Andy.
In Cucumber Quest, Cucumber's dad, Lord Cabbage, has a jerkface rating of 6 out of 5 in one of his bios. He also seems to enjoy telling people about the first time Cucumber failed him miserably.