((I should warn you that out of about 8 matrix threads so far only 1 actually got finished. The rest died.))
Name: Stan Haliburton
Hacker Alias: Jokemaster
Bio: A hacker who recently intercepted and read what appeared to be a genuine e-mail that detailed the world not being true and how to take advantage of that. Not knowing the danger it'll put him in, or the war that's going on, he decided to try it out.
Stan stood at the edge of a roof. He looked down, the building was only a couple stories up, if he fell it wouldn't be so bad. He looked over at the next roof, about 3 meters away. He took a deep breath and started whispering over and over again 'I believe, I believe I believe...." He went to the other edge of the roof, ran as far as he could and jumped.
Later, when they put him in the ambulance, he marveled at how far he got, he could almost reach out and grab the edge of the roof. He smiled. It seemed the e-mail was true. He'd just have to try again.
Vader's wife was very pregnant when she died 19 years ago. All of a sudden a 19 year old who is very strong in the force and has a distinct resembalance to him in his younger days rolls in from Vader's home planet with his old Master Obi-Wan (Who was the ONLY other person preset at the time his wife died. And to boot, the kid's last name is Skywalker.
So in answer to your question, he knew Luke was his son because his name is Darth Vader, and not Darth Retard.
-Forum post on why Vader knew Luke was his son.