Just to answer a quick question. If you watch the beginning of Alien 3, when the camera is showing off the vacant interior of the Shulako. The camera pans by an egg stuck to a beam (near the mess hall). If you watch it carefully, you'll see the egg has a barcode, or tattoo type marking on it. Which leads you to assume the egg was put there after Aliens, or was on board the whole time.
Of course this only gives us one face hugger, still don't know where the second for Alien 3 comes from.