I think Miko Ooka might be considered bi-gender, since Miko's second form is both referred to as "wolf" and "boy" form, although she's usually viewed as female.
Also, Soune Taya may be considered "male" in Japan, but is widely viewed as being bi-gendered (or hermaphrodite, although those two terms are not synonymous) or even female sometimes in the English-speaking fandom. His gender identity is somewhat a blurred line.
And also, another Ciel, Ciel Shiin is genderqueer masculine. There's also Hanshou Riley who's a transwoman.
@Snow: I think Yami having a desire to be a little girl as stated on the old UTAU wikia is means to have gender dysphoria, although that's a personal headcanon, and of course, not official since EcstacyDarks refers to Yami with male pronouns. (No doubt because of the trap thing.)
Although it's interesting because Yami's considered a trap, but genuine interest in changing genders almost contradicts it and leans towards transgendered or genderqueer. I mean people with transexual headcanons for Ritsu go off of what he wears, rather than factual statements of what he desires.
Canon obviously has cleared up misconceptions by pretty much saying Ritsu's gender is left for interpretation.
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I have plans to release an UTAU who's a transexual male, but it might take a while.