The state has an interest in licensing marriage that it does not have with same-sex pairings. Male-female coupling is the only kind of pairing that can naturally produce children, who do not consent to the relationship and will be our future citizens. The best way to raise them is in a married household with a role model of each sex.
However, for various reasons, same-sex couples may end up with children in their home. Some of those reasons government can't prevent, other reasons government can (but whether government should is debatable). I'd rather see a child raised by a gay relative and that person's partner if the only alternative is an orphanage. California-style domestic partnerships are a great way to provide protection and cohesiveness to such situations.
I think the best solution is for the states and the federal government to keep marriage licensing restricted to traditional marriage and have domestic partnerships for the same-sex situations. Perhaps even a another kind of arrangement can be made for a platonic situation where two people want to be guardians of children - such as a brother and a sister, or two sisters, etc.
Preference is custody issues should always be in placing a child with her mother AND father, unless one of them is toxic. And there should not be a right to IVF or any kind of third party reproduction - not for anyone. That is not to say it should be illegal.
http://walrus.blogtownhall.com/2008/07/23/neutering_marriag e_devalues_and_discourages_marriage.thtml