Nuriko from FY
Ritsu, Momiji, Ayame and Yuki from Fruits Basket
Subaru from Tokyo Babylon

Well... Not sure if Anyone has already said this, but I thought that Kanda from D grey man was a girl when I first saw him

Ranma Saotome from Ranma 1/2

Ayame, Ritsu, Momiji from Fruit's Basket. In fact I've seen at least 3 pics posted in female scans of Ayame.... hehehehe

kurapika from hunter x hunter

kuchiki byakuya from bleach

hyuuga neji from naruto

kurama from yuyu hakusho

jin from samurai champloo

Athun from gundam seed/destiny
Reiko from Gilgamesh

This travesty from Vandread... that's woman!

I guess blond teenage boys:
Ion (Trinity Blood), He's so much like a girl but at the same time so adorable as a boy. I love his character.
Quatre Robera Winner (Gunduam Wing) I guess he's just the male version of Cagalli! Only with softer nature and kinder personality.

Fuuchiyouin Kazuki from Get Backers....actually the first time me and my friend saw him we seriously tought he was a girl until he spoke...then we were : WTF?!

haku from naruto

Well lets see not counting the ones that acutually transform into women.

Gourry Gabriel (Slayers) was passed off as a woman (very amusing too).
Hotohori (Fushigi Yuugi)
Agito (Air Gear)
Thread Master Kazaki (Get Backers)

Yukimura Sanada from Samurai Deeper Kyo... in fact in the manga, he has a female bodyguard that looks so much like him she acts as a double for him.

Let's see, there's also yumichika from bleach, although I never really thought he could be a girl, he could easily pass for one.

Maora from Shinshi Domei Cross (The Gentleman Alliance).

Touka from Touka Gettan lolol. He fooled me in the first few eps xD

Hayate from Hayate no Gotoku definitely. And I definitely agree that most CLAMP males could pass of as females!

I honestly cannot beilieve that nobody has said Oorochimaru from Naruto yet. He's so feminine, it's almost scary
Nej from naruto (definately) and Itachi as well (hey, I thought he was a chick!)
Ashura from RG Veda (but he's kind of...genderless, so to speak)
Ritsuka and Yayoi from Loveless
most of the guys in Host Club
Watanuki from XXXholic (...don't ask. I actually thought he was a girl!)
Renji from bleach...and Byakuga as well
Sesshomaru for SURE!

Yuki Sohma

I can only think of one: Kazuki from Getbackers LOL

the main character from tokyo babylon. theres something wrong when you have an identical twin sister... kind of wierd.

hmm, Let's see, I think these ones aren't noted yet...
-Fujiwara Sai (HikaGo), actually, Akira and Hikaru themselves may look pretty if cross-dressed.
-Mikagami Tokiya (Recca)
-Hotaru (Hack/tasogare), If you read the manga, you'll find out that Hotaru is actually a boy, despite those cute voices and attitudes.
-Shen-Lon and Kai Kudou and from E's otherwise
-Fye de Flourite, even Shaoran crossdressed once
-well, there are too many I can't remember all of them

I definitly agree with Nuriko from Fushigi Yuugi... Cos he's a crossdresser to begin with.

Haku from Naruto. I was fooled just like Naruto himself thinking Haku was a girl.

Quite a lot actually. Lots of bishies can look like a girl with a dress and makeup.. But at the top of my head, Nuriko and Hotohori from Fushigi Yuugi.. ^^

Naruto if you've seen his harem jutsu.