14.07.09 "I don't know how that got to be but i'm a big supporter of the X-files and i've like seen almost every episode and not once did it mention Mulder being the father of Scull'y baby"

Can't have watched very carefully can you? William being Mulder's son is frequently referenced to in the final episode. Just off the top of my head:

Guard: "What are you thinking about?"
Mulder: "My son. His mother."

Scully: "Our son, Mulder ...I gave him up. Our son. I was so afraid you could never forgive me."

Not to mention the meaningful looks that Mulder and Scully give each other when the officiator at the hearing asks, "Agent Scully, isn't it true that you and Mulder were lovers, and you got pregnant and had his love child?"