In the one-shot Hiding in Plain Sight Harry Potter gets Lasik eye surgery and becomes completely unrecognizable to the pureblood wizards at Hogwarts without his trademark glasses. Then the Aurors try to recreate 21 Jump Street at Hogwarts. The muggleborns have absolutely no trouble recognizing the incredibly out-of-place "first-year students".
A large degree of Kirby fanfiction gives Kirby the ability to become completely indistinguishable from whoever he's taken the power/costume of, despite the obvious size differences.
In the Calvin At Camp episode "The New Kid," Larry Koopa infiltrates the camp while wearing nothing but a Mickey Mouse hat.
In Nobody Dies, in order to pacify a rampaging A.I. based on Fallout 3, Gendo tricks it into thinking he's Abraham Lincoln simply by wearing a top hat. It probably helped that he already had the beard.
Hivefled: in one of the less grimdark scenes, the four trolls with the smallest and thus most easily-concealed horns dress up as humans to go food shopping. Not only are they wearing hats and gloves in June and concealing their grey skin only with face-paint, but John only just manages to stop them talking about eating babies in public.
Zigzagged throughout Like One Sundered Star, where superhero identities are Paper Thin Disguises when they have any efficacy at all. Karkat and John are the only ones who DON'T immediately ID each other as Heir and Hemogoblin out of costume. Dave and Bro barely even give lip service to the trope, removing their shades while "on duty" but making no other effort to conceal their faces. Kanaya has to drastically redesign Rose's Seer of Light costume into a real disguise after her Superpowered Evil Side rampages through New York unmasked.
In Welcome To The Family Light Yagami determines that not even the genii of Wammy's House can withstand the mighty stealth powers of the "magic hoodie" that somehow renders him unrecognizable whenever he goes out to do nefarious things.