Laurel said:
Would the child get to make saves of thier own?
Only if specifically targetted. I would say only divinations would be able to target the child since most other spells require line of sight to the target and the child has full cover.
The child otherwise would be treated as a held object for other saving throws (esp reflex saves).
How does target spells like baleful polymorph work?
This one is ugly. Choose either: the baby is likewise polymorphed and the mother will give birth in the new form as a creature of that form; OR the baby is expelled (with no damage to either target) during the transformation and may or may not be able to survive outside the mother. The answer to this and the next question depends on how you view similar situations with swallowed whole targets. See below....
What about flesh to stone? baby remains unstoned dies without mother turning back quick enough?
I would have the baby fail automatically and if a break enchantment or stone to flesh restores the mother, then the baby is automatically restored as well.
The same applies to swallowed whole creatures. They should fail any fortitude save the swallowing creature fails. Doing it this way eliminates a lot of kooky exceptions and circumstances. Do you really want to have to guess how much is available inside the stomach of the Purple Worm after it is turned to stone? Or how many inches of stone the party has to cut through to find the swallowed companion? Yuck.
Could someone target the baby? What would it's saves be?
See above. I would give the baby an average CON equal the number of months in utero (scaled to the human 9 months for other races) and figure Fort based on the CON modifier. A fetus cannot make Reflex saves. Its Will save would be -5 since its Wisdom is no more than 1 until it attains more self-awareness at 3 post-utero months old.
Any resistance bonuses possessed by the mother apply to the baby.
Mothers are said to 'feel' thier children while in the womb. They know when something is wrong- is there a big bonus for any skill check the mother does on the kid?
When applicable, I'd give a +4 circumstance bonus to a mother's sense motive checks. But I would also give the baby a +2 aid another bonus to all skill checks (even against mom) since her instinct is to help the baby.
There are some ah- spells that are like contraceptives in the BOED I believe.... do those exsist? Are there no known plants that woman could be on or take if she knows she's going to the deed later?
Depends on the campaign. Herbal remedies (both male and female I think) are listed in the Forgotten Realms Campaign Setting book, for example.
The baby is just part of the mother since it cannot be separated from the mother without killing one or both of them. Would you penalize the wizard with an extra person if someone had a parasitic invasion, say a tapeworm? I wouldn't. I'd say the tapeworm is part of the host victim until it is destroyed.