Garland from 8-Bit Theater fits squarely in this category; he'd just as soon hang up inspirational posters in his dungeon and bake cookies for his enemies as kill them. The one time he did build a death trap, he tried filling it with acid, but the Forest Imps who live around his castle switched it with Mountain Dew. (Forest Imps, incidentally, are the only creatures Garland will go ballistic over. No small wonder, since they tease him all the time and he can't convince anyone that they're messing with him.) He has his moments though. The best one being when his underlings decided to mutiny, and have a meeting about it. It appears that Garland, in true Laughably Evil fashion, is catering the meeting and made tacos just for the occasion. When the smarter minion calls him out on it, he casually breaks down the reasons why the mutiny will fail, and then reveals that the tacos were full of amnesia peppers. "In 10 minutes this meeting will have never happened." It could also be because he is incredibly thick and doesn't know how to be evil.
Which makes you wonder, is he just not very good at evil, or is he Genre Savvy enough to realize that being a competent villain is typically a death sentence in an RPG Verse?
General Tarquin. Just listen to him describing how he managed to create those big, flaming letters to celebrate that his son has returned. All while telling said son just how much he means to him.
Tarquin: "I mean, the prefects only informed me about the escaped palace slaves around dusk. My men had to get out to the mountains, recapture them, nail them into position, and then get the oil out there in time to light the rebellious little pricks on fire in unison. It's really pretty impressive, logistics-wise, when you think about it."
Malack, Tarquin's former adventuring buddy and current Evil Chancellor, is also very much Affably Evil. He gets along very well with Durkon, and may even be more genuinely nicer than Tarquin, even though he's also Lawful Evil. Having lost several children violently, he also has very mundane woes that he openly discusses with fellow parents. Except those children were revealed to actually be vampires, meaning his "special bond" was of a much more nefarious nature.
Malack: ...and Tarquin keeps telling me that if I want more children so badly, I should just find the right person and get to it, but...I don't know. Vaarsuvius: Have you ever considered adoption? Surely your political climate produces no shortage of orphans. Malack: Yes, but...I'm worried about not having that, you know, special bond...
Thog is generally Affably Evil when he's not being Ax-Crazy. On at least one unfortunate occasion, he was both at the same time.
Thog: Yay! Resisting arrest is fun!
Hilgya is friendly and likes to flirt with Durkon and doesn't seem to hold the Order in any real malice. However, she's willing to stand by while Nale butchers an innocent Fae so she can steal the talisman Nale is looking for, lets her companions ambush the Order, including her would-be boyfriend, and revealed in her backstory that she tried to murder the dwarf she was in an arranged marriage with (and while being in an arranged marriage is hardly conducive for the happiness of a free-spirit like Hilgya, the fact that her husband was friendly towards her and she opted for murder first instead of just running away like she would do anyway does not reflect well on her attitude toward sentient life). She is Chaotic Evil, with far more emphasis on the Chaotic.
How about the Three Fiends: Lee, Cedric, and Nero? They persuade Vaarsuvius to give them access to eir soul for a few, to destroy many of the black dragons on the planet (and by extension, the Draketooth clan), and so on - but they're always polite, sensible business-oriented individuals.
Headon from Tower of God. He withholds information, plots against the Tower and the ruling system and thus brings pain into Baam's life, but he sincerely welcomes Baam and anyone with enough balls to climb the Tower with a smile.
Dom from Megatokyo is an old college buddy of Piro and Largo, and has even loaned them money when they were in a tight spot. He is also a ruthless corporate enforcer who can get quite menacing on occasion.
Ongoing Completed imageboard Choose Your Own AdventureRuby Quest has Red, who dresses nicely, helps you with his cane, and warns you not to ask questions or he'll have to rip your throat out.
Satan from Casey and Andy seems like a nice person (and she's very cute), but is still the lord of all evil and not unwilling to capitalize on it. Amusingly, she could almost always solve the problem at hand with a flick of her hand, but chooses not to, because she likes the evil schemes of the villains. But woe if they harm her boyfriend...
The Varn Gene Mage from Terinu is pleasant and forgiving of his Dragon's occasional failure, and is utterly appalled at how one of his allies treats her prisoners. Oh, and he's responsible for a few billion deaths during the original invasion of the Earth. No biggie.
The Beelze family (except Diva herself, who is just affable) of Evil Diva. Notably, her father. He's an all-around nice guy who bakes cupcakes for his daughter to share with friends at school, and he is also the guy who you sell your soul to in exchange for fame/fortune/doughnuts (he likes watching TMZ to "catch up with old friends"). Satan himself might also qualify...or maybe being affably evil is just a requirement for all of Hell's employees, as it certainly makes it easier to corrupt the righteous.
Pretty much everything that talks in the Dungeons & Dragons-influenced comic Speak With Monsters at least reaches this level of goodness. Some monsters break the fourth wall to brag about how useful they are to DMs, some argue that their actions are justified in the long run, and some just get Pet the Dog moments between ripping out humans' hearts.
Captain Snow from Archipelago, psychopath, pirate, evil to the bone. Yet chats amiably to the heroes as he rips out their souls, threatens pregnant women, and tries to bring about the end of the world. He will even stop in a battle to talk about opera or books. He enjoys a good cup of tea and once stopped a murder and pillaging to enjoy a cup of it at a local tea house... as the buildings around it burnt to the ground.
And his last act before dying was to save the life of one of the protagonists.
Pretty much all the main characters in Yet Another Fantasy Gamer Comic. They are all technically evil monsters, but that doesn't mean they spend all their time doing evil deeds. Arachne the drow will give you sensible relationship advice...then return to her dungeon to torture her collection of captives. Lewie the lich will lend you some skeletal minions to help out around the house...then attempt to Take Over the World through mind control. Good old Mrs. Bloodhand is the nicest, most motherly orc you are ever liable to meet...but put her in a position of power and she turns ruthless and Machivellian. Put her in a battle and she turns deadly.
The Draconian Dignitary is incredibly ruthless, but two of the three versions we've seen have been surprisingly generous and kindly when not blasting chunks out of the planetary surface or murdering people - the Alternian version, Diamonds Droog, spends most of his time as Aradia's exile encouraging to go with her feelings and congratulating her (although things on which he was congratulating her are questionable), and the post-scratch version gets along extremely well with Jane's Dad and makes sure he gets plenty of shaving cream and pipe tobacco in his Luxury Prison Suite.
In Cthulhu Slippers most of the Old Ones are this, with the exception of Hastur and even then he gets better after coffee.
In The Dragon Doctors, Cary is so charming in person that it's easy to miss that she is a criminal mastermind who feels few compunctions about killing or crippling anyone in her way — or, for that matter, about the massive collateral damage that some of her schemes cause.
The Shadow Child aka Disbelief from Roommates comes off as this. He is even genuinely empathetic to and disturbed by the suffering his very existence causes. And then turns around and describes in great detail how he intends to destroy his enemies (or yours if he likes you), so he obviously enjoys this aspect of being a personified negative emotion, even if he regrets some others. He is also cuter than a creature like him has any right to be.
And that's meta comic with a cast mostly composed of Retired Monsters (and Retired Badasses) so the trope can be applied to almost all of them in one degree or another. But the kid still stands out.
Grrl Power has Vehemence, who strikes up a friendly battle commentary with Sydney when she goes to see why he's just watching the fight, agrees with her that "For Whom the Death Tolls" looks like a total dork in that cheesy costume, wishes her well when she leaves, and turns out to be the mastermind of the entire supervillain attack.
Tork, the Geckoid thief from tinyraygun, especially compared to his egomaniac of a sidekick, Vector. He's surprisingly laid back about stealing Nepta's stuff, and isn't even all that interested in Nepta herself.
In Godslave, Turner attempts this when playing Come Out, Come Out, Wherever You Are with Edith, trying to convince her that he's not interested in killing her and only wants Anpu. Given how he has already tried to murder her twice at this point, it's not very effective.
Posey in The Sanity Circus is Affably Evil towards Attley - she talks constantly of trying to help her, and still smiles and talks like they're just as good friends as they were before it turned out Posey is an Eldritch Abomination in human form. To everyone else, though, she is only Faux Affably Evil at best.
Angel Moxie: Tsutsumu, so affable that after his defeat, it turns out he arranged for the heroes to get all his stuff.Frigg. Syr'Nj, too, although she's not as obviously female.
Guilded Age: Iver, Savasi Warlord, doesn't really make much effort to hide how much of a Smug Snake he really is and how clearly he's just using the World's Rebellion to make himself rich, but at least he's charming about it. On the Gastonian side of things, His Grace Iwatani is a Manipulative Bastard extraordinaire playing the cultists and his own allies against each other to advance his own agenda, but at the same time he puts on a friendly and concerned facade to whomever he's speaking to, he's shown nothing short of frank admiration for how well Syr'nj has handled herself as a member of the Heads of Houses, and he's a genuinely doting father to his son, Taro.