Verified answer

Something like this?

Maze The Megaburst Space

http://www.youtube.com/watch?v=WdUlat6HcHk

The quality isn't as bad as that video btw.

@Neane: Ah! How could I have forgotten Ren/Run & Rito/Riko from To Love-Ru

There's one anime that has a girl cross dressing, It is Revolutionary Girl Utena.

Most Feminist Anime ever.

There's Cinderella boy. It's about a guy and a girl that get fused into the same body, and each day at midnight one of them takes over. In Simoun, everyone is born girl and can turn into a boy if they want to.

Le Chevalier D`Eon (man shares the soul of his dead sister, occasionally transforms into her)

Also, there's Tenshi na Komanaiki. It has to do with a boy wanting to be the the most manly man but got turned into a girl.

There's also To Love~Ru.If you want ecchi. Several of the cast change bender.

http://www.youtube.com/watch?v=gMrUx2Sq7xI

I only think that this is a manga so far, but i think that it's pretty good, too bad not many people know it.

It's called Ai wo Utau Yori Ore ni Oborero. This is a story about Mizuki and her group of girls that go to all girl school. They are called the "Princes" because they look handsome and masculine They look and dress like guys and they are a band. They are admired and loved by their many female ans. But they also have another admirer, his name is Akira and he attends an all boy school, in that school he is called "Princess" because he looks very cute and feminine. the main charcters of this story are Mizuki and Akira

Kampfer: the main protagonist was chosen to be a kampfer but he needs a body of a girl to be able to use his powers

Kino's Journey: the main protagonist is a girl but she dresses like a boy

Tenshi na Konamaiki: Its about a girl who used to be a boy :P

Ginban Kaleidoscope: Its about a figure ice-skater girl who was possessed by a ghost canadian pilot boy.

Otome wa Boku ni Koishiteru: The Granfather of the main protagonist wishes him to attend an all-girls school.

Ok. Here's one I don't hear too many people mention but I kinda liked. Testuwan Birdy Decode. A space police woman accidentally kills an earth dude and she offers to let him use her body until his gets repaired. It switches between his and her form a lot.

As for crossdressing there's;

otome wa boku ni koishiteru

Working!!

but they are guy --> girl.

mayo chiki! its new so it only has 5 episodes