Doctor Who: If you're overweight, there's a good chance you're actually a disgusting fat alien in disguise (Slitheen, Abzorbaloff, etc.)
Also the Marshal from "The Mutants," an obese human colonialist who refuses to relinquish his power over an apartheid-like regime.
Or maybe you're stealing food rations during WWII.
However, basically subverted in the Eighth Doctor Adventures books. The Doctor's Worthy Opponent Sabbath (who serves as an expy of the Master, but more reasonable) is rather on the chubby side of Stout Strength, because he just doesn't care about his appearance (for the same reason, his hair is so short as to almost count as Bald of Evil). Once in a while, other characters make unflattering remarks about it, but only rarely. And it provides for an excellent Paper-Thin Disguise opportunity in one book, where with a suit which is only slightlyBigger on the Inside, he almost effectively disguises himself and proves that the Doctor doesn't realize that humans can lose weight or something.note ‘Your suit distracted me for a while,’ he added. ‘I couldn’t understand how you managed to squeeze your rather ample form inside it.’ He falls just short of being Affably Evil, and has a number of Enemy Mine situations (and quite a lot of Foe Yay) with the Doctor. He just happens to be quite evil and quite large.note And Big Eater Fitz, who is in actual fact described as looking like he's "made of pipe cleaners", seems to eat more than he does, so Sabbath is hardly a Villainous Glutton.
Also subverted by the Adipose. Sure, the species are comprised of fat-cells, but the villain helping them get born is extremely thin and the only way for them to breed is for people to lose weight. If people were happy with how fat they were, there would have been no problem.
There's a character on Freaks and Geeks who's overweight, a geek, and has a medical condition that makes him smell bad. The three main Geeks avoid him for the first half of the season, but once he is paired with Sam (instead of Sam's crush) he confronts Sam, and he is seen hanging out with them occasionally throughout the rest of the series.
Interestingly enough, in a flashback episode, the character was described by Phoebe as "cute naked guy" who was just starting to put on some weight. By the time of "The One Where Monica Gets a Room-Mate", he was fat.
Exception: on House, Chase is called out repeatedly for being a jerk on the subject of the overweight patients he treats. In a later episode — "Que Sera Sera" — the team's conviction that their patient's morbid obesity was responsible for his ailment caused them to come quite close to not diagnosing it at all.
Averted in LOST, which has been fairly sensitive dealing with Hurley's obesity. While not often addressed directly, a major part of Hurley's character is guilt related to his weight. He was previously involved in a deck collapse in which two people died. He refuses to ration the food, then is found to have hoarded some. In the fourth season finale, Frank comments that the helicopter needs to shed a few hundred pounds. The camera focuses on a conflicted Hurley, and then Sawyer jumps from the helicopter so Hurley won't have to.
Fairly sensitive? Maybe in season 1, when Hurley was a character with many traits (decent, kind, somewhat crazy, obsessed by the numbers...) who also happened to be fat. In season 2, his being fat became the focal point of his character - the most important thing about him, what caused his mental illness, his Fatal Flaw, etc. And all those Sawyer fat jokes - sure, James was still a Jerk Ass, but Hugo's weight was by far his favourite target. Then there was that bit about Libby falling in love with him, and after she is revealed to be a former patient in a mental hospital - implying that an attractive young woman would fall for an obese guy only if she's not completely sane. After season 2 it got better, admittedly.