Yukari Is Free has Nai'tyrrus/Ghostmaster, political ambassador of the Veluszhi Imperial Military, and definitely the most polite of its three leaders, unlike his compatriots Warmaster and Nerdmaster. This is best exemplified during his attack on Hawaii, where he politely takes tea with and speaks courteously to Sasuke and Rei, even while his ghost familiars are destroying the city, and he even fully admits that he's only keeping Sasuke and Rei around until they bore him.
In Downfall, most of the villains are motivated by truly noble intents. Of course, any fic that has Unohana, Ukitake, and Kyoraku working to overthrow the Seireitei...it's a given. Bonus points for making Aizen, Gin, and Tousen the good guys. Realistically. By the time the reader's done, they want Seireitei burnt to the ground...
In False Smiles, the Scoobies manage to stop Mayor Wilkins' ascension by first finding out exactly what he needs to do and when he needs to do it in order to ascend in the first place, and then stopping him from meeting all the requirements. At the end of the story, the Mayor, who is still technically invincible and immortal, actually congratulates the Scoobies on a job well done, and thanks for being such fine upstanding examples of young people taking an interest in the safety of the community. He also remarks that he'll just wait around until his next chance to turn into a gigantic man-eating snake demon. In the mean time, he tells them, he's going to concentrate on civic improvement and keeping the "bad elements" out of Sunnydale.
Continuing Aleine Skyfire's trend (see the Sherlock Holmes listing below), Colonel Moran is made even more complicated in Children of Time, trying to rape a 17-year-old girl before he kills her and yet respecting that same girl's unconditional love for Holmes. And speaking genuinely normally with Holmes while torturing him. Yeah.
In the same series, Professor Moriarty is Faux Affably Evil, and yet he has his moments in which you get the feeling he just might be sincere.
Which is taken up to trueAffably Evil with his clone in the second season. He has rather less of a vendetta against Sherlock, and is something of a fairly polite and definitely respectful Stalker with a Crush towards Beth Holmes.
In Game Of Touhou, a lot of villains are very affable: Seiga will casually hand one of her whores to others (until she breaks down), Yukari is soft-speaking, Yuyuko enjoys chatting with the smallfolk.
In Royal Heights, the main antagonist Embry is quite the educated and polite Hot Witch with a classy wardrobe and even classier personality. She has a penchant for manors, offers tea to her visitors, and is incredibly gleeful and passionate about her plans to destroy an entire dimension.
In Origin Story, there's Magneto, in the appropriately titled Chapter 21: “Breakfast With Magneto”.
Quirrell and Voldemort sing, dance, pick up girls, and watch She's All That in between plotting to murder Harry. Oh, and one of Voldemort's Horcruxes is a Zac Efron poster.
The Dementor shown returning Quirrel's civilian clothes was also quite nice.
The sequel has Lucius Malfoy and Dolores Umbridge. The former avoids walking at nearly every opportunity, preferring instead to show off with increasingly complicated ballet moves; Umbridge comes off as an odd mixture of Southern Baptist preacher, yandere, and drill sergeant. And she's played by gorgeousJoe Walkernote who played Voldemort in AVPM.
In Queen Of All Oni, Jade's personality is more or less the same even after her Face-Heel Turn, other than having fewer morals (and wanting revenge on Tohru for becoming Uncle's apprentice instead of her). For example, when she has Ozeki attack Section 13, she gives him specific orders to NOT kill anyone, and she broke the Dog Talisman to make Scruffy immortal again, for no apparent reason other than pampering her pet. Also, she pays the Enforcers regularly (and apparently it's a lot of money), and doesn't torture them like Shendu and Daolon Wong did, and even AFTER she gave Chow the code-name "Bonkers" for suggesting they rename one of her plans, they STILL feel that she's a better boss than Shendu (probably better than any boss they had in canon come to think about it), so much so they agree instantly on it.
In Perfection Is Overrated, Meiko Moriya might be pretending to be Mai's friend but remains relatively courteous and polite to her after Mai blows her and Bachiko's cover by realizing that they weren't friends. She even apologizes for being relatively familiar with someone she's just met, and goes from calling her "Mai" to calling her the more polite and formal "Tokiha-san".
In Dark World, Rancor, Discord's little sister, is a Friendly Enemy towards the mane cast despite the fact she's one of Discord's Co-Dragons and a Blood Knight who is looking forward to her turn to fight them. She does things such as asking Rarity for her autograph (she's a fan of Rarity's past life, Melody), commending them on their fights, and even giving Apple Pie the last pages of a comic the Valeyard used in a Break the Cutie on her, revealing it was a Bittersweet Ending and not a Downer Ending for seemingly no other reason than to Pet the Dog. And while she is vicious when she actually fights them, she spends the majority of the fight talking to them politely. And hitting on Spike. Justified as she's a Punch Clock Villain who has no actual grudge towards them and is only doing this because her Father told her to.
In the Pony Dot Mov series, we have (yet again) Fluttershy! It seems that every time Fluttershy is portrayed as a villain she's depicted as this, although that's hardly surprising when you consider how she is in canon. To drive the point home, she never even swears (whereas the others are shown to all curse like drunken sailors) not even after she snaps and becomes a chainsaw wielding psycho!
It should be noted he told them to try to escape over dinner too.
In Gender Confusion, it's difficult to distinguish who the bad guys really are until one of them actually goes out and commits a canon atrocity... and then you still need to remind yourself that, yes, they were the ones in the wrong.
Luminosity's lower-ranking Volturi are all like this. The worst is Jane, who is best defined as amoral—if she hits you with her power, then she looks at you funny if you scream.
In The (Not So) Short Second Life of Bree Tanner and its companion piece, Ashes through an Hourglass, Alec from the Volturi comes across as charming, insightful, and sympathetic, without betraying his more villainous tendencies like manipulating Bree, showing a general indifference to human life, and casually ploting and rationalizing murder.
The larger portion of reader reviews consider Alec not just amusing and appealing but actually persuasive in his outlook on being a vampire, which is almost always in stark contrast to the noble ideals and humane lifestyle of the Cullen family.
Kyrio Streika, from New Dawn. He is always polite, always serene, never once raises his voice or even curses. He is always friendly and even helpful to Matthew and company, which makes sense, given Matthew is his son. He is a devoted family man, despite having difficulties that he came across during his occupation of choice. He also happens to be rather like Sousuke Aizen in several ways, including being very disturbingly violent in contrast to his eloquent words and actions, and having plans within plans, effortlessly manipulating most everyone he comes across and killing the rest, all for the good of his dear son.
Gravity Falls Rule 63: Bonnie Gleeful. She's a very sweet lady, even when she's killing you with her own two hands.