i used zofran during my 3rd trimester without ill effects.
I am 20 weeks and have been on Zofran for about 9 weeks - I am a teacher and running out of class to puke just doesn't work with 2nd graders! I just take 1/2 of a pill in the morning and I'm good to go. I've gotten overly confident a few times and tried to go off of it, but every time I end up puking all day, so I'm stuck for a while. Luckily, I'm family friends with the head of a NICU and he has assured me that there are no side affects for baby - all of my appts. have been very healthy so far!
P.S. - it can cause pretty bad constipation, so up your fiber intake!