User blog comment:SuperFlash101/"Phineas-n-Ferbenstein" nominated for Emmy/@comment-961279-20091016184445

This news is a little late, but the answer I got back from Dan is that neither Phineas and Ferb nor Spongebob won. For this category, the winner would have had to have received two-thirds of the vote.

So, it's a little sad that neither won, but it does reveal that both nominated shows were very strongly-written.