If she wants to go organic, is she also planning on cloth diapering. I didn't use cloth diapers but I know they are making a MAJOR comeback. There are also patterns for really cute cloth diaper covers. Even if she would only use them while at home it would really cut back on the cost of diapers.
I could not have lived without my bottle sterilizer. No boiling bottles for me.
Clothes for all stages are great. It was really nice to have some new clothes on hand for when baby outgrew her clothes.
Here is one I always think about: A certificate for a massage for mom. After carrying around the baby for so long and then tending the new little one, mom will really need some "me time". Or a mani/pedi. That would feel awesome to those poor pregnant hands and feet.