I had the four at the hospital, but before that I had my male sim get abducted by aliens (twice) and have the babies at the hospital.
So:
1) Father gets abducted twice. Both babies are born at the hospital. Both babies live in the alien bassinet with alien clothes. Both babies age up to be blue alien-looking sims who can don and change their disguises.
2) Father marries purple alien. They both become pregnant.
3) Mother has one purple baby at the hospital. The baby lives in the normal bassinet wearing alien clothes. When it ages up, it is purple, has normal eyes, hair, and facial features. It cannot put on its disguise and it wears normal clothes. According to my other sims, it are not a "Known Alien."
4) Father has triplets. The babies live in the normal bassinet wearing alien clothes. When they age up, they are purple, have normal eyes, hair, and facial features. They cannot put on their disguises and they wear normal clothes. According to my other sims, they are not "Known Aliens."
Does that clear things up?
EDIT: I figured it out. I don't know WHY but the game doesn't register half-bred aliens as being aliens, so it gives them alien skintones, but no alien abilities (including the ability to mask their godawful skin tones with a disguise). I REALLY hope that gets changed in the future. I'm not the only one who seems peeved...
http://www.modthesims.info/showthread.php?t=552392
http://www.modthesims.info/showthread.php?t=552724