Obviously, as all female roles were played by men in Elizabethan times, there were technically a lot more cross-dressers in Shakespeare, but these are the ones that cross-dressed in the context of a play. Viola and Rosalind are the really plum roles, but one of my personal favorites is Innogen from Cymbeline. She is really put through the metaphorical wringer. Special mention to Julia, who exclaims "O ME UNHAPPY!" and then faints dramatically, which, if you're going to faint, is the way to do it.