Well, the obvious place to start would be by examining the character of Viola, and how she appears to be a man, but in reality is a woman. This of course extends to other examples of appearance vs. reality, as her twin brother appears to be to all intents and purposes Cesario, whilst in reality being somebody very different. However, apart from these examples, one of the best quotes I think in the whole novel that relates to this important theme comes in Act III scene 1, when Viola discusses the role of Feste, and how he appears to be a fool, but in reality shows himself to be incredibly wise. Note what she says:
This fellow is wise enough to play the fool,
And to do that well craves a kind of wit.
He must observe their mood on whom he jests,
The quality of persons, and the time,
And, like the haggard, check at every feather
That comes before his eye. This is a practice
As full of labour as a wise man's art;
For folly that he wisely shows is fit,
But wise men, folly-fall'n, quite taint their wit.
This quote relates to the way that being a "fool" paradoxically requires great wisdom and great effort. Feste is a character worthy of attention, because, if you analyse his role very closely in the play, he is very definitely not what he appears to be.