Cain was the first nephilim. He was the seed of satan. The Bible does not say everything but all we know is that the devil beguiled/seduced Eve. What happened after that is superfecundation. Conceiving twins from different fathers.
Lanolin already posted the part where Cain came from.
Genesis 4:1 And Adam knew Eve his wife; and she conceived, and bare Cain, and said, I have gotten a man from the Lord.
Nothing there about Satan knowing Eve.
3 And in process of time it came to pass, that Cain brought of the fruit of the ground an offering unto the Lord.
4 And Abel, he also brought of the firstlings of his flock and of the fat thereof. And the Lord had respect unto Abel and to his offering:
5 But unto Cain and to his offering he had not respect. And Cain was very wroth, and his countenance fell.
6 And the Lord said unto Cain, Why art thou wroth? and why is thy countenance fallen?
7 If thou doest well, shalt thou not be accepted? and if thou doest not well, sin lieth at the door. And unto thee shall be his desire, and thou shalt rule over him.
Do you really think that God would accept an offering from one of Satan's seed? Yet God promised Cain that if he did well, his offering and he would be accepted.
I don't think the Serpent-seed doctrine has any legs.
1 John 3:12
12 Not as Cain, who was of that wicked one, and slew his brother. And wherefore slew he him? Because his own works were evil, and his brother's righteous.
Note that the passage does not say "because Cain was conceived of the devil", but rather, "because his own works were evil, and Abel's righteous".
Gen 3:15
15 And I will put enmity between thee and the woman, and between thy seed (antichrist) and her seed (Christ); it shall bruise thy head, and thou shalt bruise his heel.
Just as Jesus was not born directly from Eve, neither does the devil's seed need to be born directly from her. Christ came some 4000 years later. The nephilim certainly were around before the time of Christ, but the bible speaks clearly that these were the offspring of women and angels, and God puts an end to these with the flood.
2 Cor 11:2-3
2 For I am jealous over you with godly jealousy: for I have espoused you to one husband, that I may present you as a chaste virgin to Christ.
3 But I fear, lest by any means, as the serpent beguiled Eve through his subtilty, so your minds should be corrupted from the simplicity that is in Christ.
The context here is spiritual. Just as the serpent beguiled Eve about what God said, Paul didn't want the serpent to beguile the Corinthians, and have them follow a false religion. If you demand that the reference to beguiling in the passage be interpreted sexually, then to be consistent, you must also accept that the devil had in mind to seduce and rape each one of the Corinthians. Bizarre...
John 8:44
44 Ye are of your father the devil, and the lusts of your father ye will do. He was a murderer from the beginning, and abode not in the truth, because there is no truth in him. When he speaketh a lie, he speaketh of his own: for he is a liar, and the father of it.
Exactly. Jesus is talking spiritually. Not literally. Each of those Pharisees had fathers, they weren't all bastard children of single women who had been seduced by some mysterious snake.