My wife went on the birth certificate, we live in VT where same-sex marriage is legal and they have redone the birth cert. forms so that there is a place to put "parent's name" it doesn't specify father. Then when they sent us the birth certificate they had changed it so that my wife was listed as father, we sent it back and had them fix it & her birth certificate now has me as "mother" and DW as "parent". We ended up getting a second parent adoption as well, there is a thread I started when I was debating if I needed one, and we decided it was important even though DW is a legal parent in VT, that does not apply federally without the 2nd parent.
Quinnsmommy: When we did the second parent adoption our lawyer (she is an expert on same-sex adoption so she knows what's up) said their was no reason to bother getting our donor involved even though he is a close friend and was happy to sign, she said he didn't need to. She said that since he is a donor and had no intention of parenting, and also is not on the birth cert. that we could just go ahead and do the second parent adoption and completely leave him out of the process. We did and had no problems. We did a home insemination, BTW.
Sorry I just realized how old this thread is but I figured I'd post this anyway, would love to here how things worked out!