I think the most obvious example is Hourou Musuko which aired last season. It's about two students (one male, one female) who want to be seen as the opposite sex. It deals with a lot of realistic issues, it's very interesting, and the art is amazing!
Ouran high school host club - girl dresses up as a male 'host'
Princess Princess - 3 guys dress in girl clothes as the 'princesses' of their all-boy-school
Kampfer - A guy turns into a girl every time he needs his 'kampfer' abilities
Plus Aoi Futaba from You're Under Arrest!, Hibari-kun from Stop!! Hibari-kun!, Fudou Gonzaburou from Kaichu!, Criff Cay/Kei from Infinite Ryvius, Ana Gram from Phi Brain, and Kaoru Hanase from Tamako Market.