Probably Haruhi, but only because I want to see Kyonko animated. I'd rather Haruhi stay a girl though, because her personality on a guy isn't cute at all. She becomes a guy who routinely physically and mentally abuses a girl half his size.

Eden of the East.

Take my word for it, that show would have so many more fans if it were genderswapped.

>>2980
But then they'd need a new pun besides johnny.

>>2981
Ahh, completely forgot about that.

Now I'm sitting here trying to think of an appropriate pun.

Kaiji (or any Fukumoto anime/manga), just because I would actually like to watch for once an anime that primarily has a female cast AND their character designs are unconventional instead of the usual bishojo/sexy/kawaii designs.

Marimite and Strike Witches

Also Madoka, Strawberry Panic, Simoun, Princess Tutu, Sailor Moon, Cardcaptor, Precure, Shugo Chara, Utena, Azumanga, K-On, Lucky Star, Hidamari Sketch, Nana, Ouran, DMC, Saki, Bamboo Blade, Ika Musume, Sketchbook, GA, Aria, Ichigo Mashimaro...

Seriously though, Hellsing and maybe Seitokai no Ichizon.
... Actually, possibly every show with male lead ever (with very few exceptions).

Ore no Imouto ga Konnani Kawaii Wake ga Nai would be interesting with switched genders. Samurai Champloo could be entertaining, too. My favourite genderbent character is Shinjiko, though.

Gundam Seed
Legend of Galactic Heroes