I think that with Thalidomide there were 2 types... both marketed as the same drug. From what I remember reading, the molecules were like, "right hand" and "left hand". There were slight variations in the medicine and the women who took the right-hand type were fine, but the women with the left-hand type had children with horrible birth defects. I should just Google this instead of trying to recall stuff from dusty, cobweb-ridden corners of my brain.
This is roughly accurate, if I remember my organic chemistry correctly. Thalidomide has two enantiomers (the "right-handed" and "left-handed" molecules), which were sold in an equal mixture of "right" and "left"; the right was effective, but the left was teratogenic. However, the wrinkle comes in in that (as a quick Wikipedia check reveals to me), these enantiomers can interconvert in vivo -- in other words, even if someone is administered only the safe, effective enantiomer, it may convert to the teratogenic one spontaneously and thus still present teratogenic problems. It's looking like this is another one of those drugs pregnant women should just avoid...
On this subject, I believe I've mentioned that I worked extensively with finasteride (the active ingredient in Propecia, which you may recall being marketed with those giant "Pregnant Women Should Not Come Within Fifty Feet Of This Medication, We're Serious" warnings) during my undergraduate work, and I'm fine. Of course, I probably won't be pregnant for some time...