With the right disguise, Agent 47 (Hitman) can blend into any environment almost perfectly.
Camille Leon (Kim Possible)
Robbie Rotten (Lazy Town) claims himself to be the master of disguise, having a costume for every possible scenario
Arsène Lupin III's (Lupin the 3rd) talent with disguises borders on the superhuman, with him able to flawlessly impersonate any man or woman in face, voice and costume, sometimes in mere seconds.
Chameleon/Dmitri Smerdyakov (Marvel Comics) has not only masks and costumes, but has gadgets that allows him to mimic superpowers (if he impersonates a superhuman).
Hydra (Marvel Comics) has agents working all over the world. Masters of disguise, they can blend in almost anywhere as a group of assassins disguised themselves as police officers when plotting an attack on Nick Fury.
Decoy Octopus (Metal Gear Solid)
Queen Chrysalis (My Little Pony: Friendship is Magic)
Obito Uchiha (Naruto) proved himself to be a consummate actor, fooling everyone he is the happy-go-lucky idiot Tobi, then the globally-feared Madara Uchiha.
Duplica (Pokemon) is a girl that can disguise herself as anybody in matter of seconds.
Copycat, (Pokemon) like her name implies, copies people's looks just for the fun of it!
Sedusa (The Powerpuff Girls)
VFD members like Count Olaf (A Series of Unfortunate Events) are highly trained to become masters of disguise.
Sly Cooper (Sly Cooper), is in the art of disguising and fooling others.
Through the act of innocence, Dain (Deltora Quest) was capable of convincing everyone around him, even the audience, that he was the rightful heir of King Adin, destined to wield the Belt of Deltora to defeat the Shadow Lord and save the kingdom from his tyranny...
...when in fact, he was a sadistic spy created by the Shadow Lord whose goal was to undermine the heroes' efforts once and for all, and no-one ever suspected this until he revealed it himself.
Al the Actor (Top Cat)
Mimic (IDW's Sonic the Hedgehog), disguised as Sonic.