done a lot of baby photographs lately with the 50 f/1.4 and 85 f/1.8 ... when they're really newborns, 85 f/1.8 is definitely the better choice. for closer-up shots (eyes, fingers, feet) either a 100mm macro or the 70-200 f/2.8 will work well to get some selective focus shots, as long as you have enough light to get good focus.
not sure which camera you're shooting with, but I've found my 5D Mark II's autofocus struggles sometimes with how smooth baby skin is, if you're not putting an AF point right on an eye, nose, or finger it just doesn't hit accurately (although if you're shooting shallow DOF you probably are focusing on those sorts of things anyway)