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As best I can remember, when people in the real world (or the supposed real world) went into the Matrix, they always looked the same in the Matrix as they did in reality.
Was that always the case, or were people able to adopt false appearances, perhaps to deceive agents or other humans? Or were there cases where the Matrix gave them different appearances for its own reasons?
The claims in the Matrix Wiki's article on Residual Self Image is a bit difficult to follow:
Zion operatives who re-enter the Matrix appear as avatars with appearances that can be totally different from their true appearance within the real world.
"Appearance" here probably means clothing and hairstyle, not physiology. The former aspects of appearance can and do change. Clothing, it seems, can be loaded at will. Hairstyle seems to reflect the person's self-perception (like Neo's in the sequels).
A person jacking in could probably manage a false mustache but not much more. It seems their physiology is picked for them by the Matrix itself. The only exception I can think of is Bane. After the infection, he looked like Smith within the Matrix, but obviously, looked like himself in the real world.
I know this question has already been answered, but I want to contribute a little fact I read yesterday (I believe it was on the IMDB).
Apparently, the character Switch was supposed to be split for two actors--a female actor in the real world and a male actor when inside The Matrix. Hence the name "Switch", I suppose. In this case, a person's residual self-image can be totally different. We don't yet know why this was changed for the actual movie. So even though it's not officially part of canon, the idea is there.
IMDB: The Matrix (1999) Trivia
When Belinda McClory auditioned for the role of "Switch", she was only going for half the role. The character was originally planned to be played by androgynous actors. In the real world, it would be played by a male actor and in the Matrix be represented in a female form, hence the name "Switch". Warner Brothers refined the idea and McClory ended up getting a single female role in both environments.
Richard found an example from the Matrix comic "Burning Hope" where a little girl had an appearance in the Matrix as an adult man, see his answer here. The top image below is what she looked like in the Matrix, the bottom image shows her real appearance in Zion.
