I pulled this because that series subverts and averts the trope more than it plays it straight. With the added bonus of the entry being nattery.

• In Naruto almost any ninja whose special abilities involve some sort of physical abnormality is a bad guy. The average member of the Sound village is likely to have some sort of implant that they use as a weapon, and a large number also have cursed seals who's second stage gives them monstrous forms. Villains with sympathetic origins who turned evil were originally normal looking, but have grown deformed (Sasori, Pain). Villains with no sympathetic angle include a shark-man, a guy covered in mouths, and a guy with a patchwork body that's filled with ropes.
  • While their bodies are quite deformed, both Sasori and Deidara's (the aforementioned "guy covered in mouths") faces are quite Bishonen. As a side note, the members of Akatsuki weren't even originally planned to be human, which has a noticeable impact on the average member.
  • Jugo is a great demonstrator of this as he looks monstrous only when he's evil.
  • There are only two ninja clans in Konoha whose abilities involve any form of physical abnormality; the Akimichi clan and the Aburame clan. Choji Akimichi is constantly derided because of his weight, even though his powers require him to be heavy. Shino Aburame's body is filled with bugs, and he uses them to great effect. He is among the least commonly shown of the Rookie 9, and his most notable trait is that everybody seems to think he's creepy This actually exacerbates the trope, since Aburame wear trench coats to obscure the openings for their insects and the Akimichi just look fat. there's also the Hyuuga, with their blank white eyes that have bulging veins when activated, which have a house system that screws you over if you're a second-born or the descendant of one. not actually EVIL, but once again, this is the token "good guy" village.
  • Of course, there's also the matter of three of the most disgustingly evil men in the Naruto Universe, Hidan, Madara Uchiha (at least used to, and Sasuke are all quite good-looking, so there's some subversion. Kisame might not have a sympathetic angle, but he's at least Affably Evil.

I think someone suggested a Good Is Sexy redirect to this as an alternative on a suggested YKTTW. Would it be a bad snowclone?