As creepy as this sounds (and as offensive as it is to modern sensibilities) there does seem to be a strong tradition for interpreting Genesis 6.1-3 as having to do with angelic beings having sexual relations with female humans.
There is some speculation in the Jewish tradition regarding this text. The author of 1 Enoch writes, “And it came to pass when the children of men had multiplied that in those days were born unto them beautiful and comely daughters. And the angels, the children of heaven, saw and lusted after them, and said to one another: ‘Come, let us choose us wives from among the children of men and beget us children.” (6.1-3a)
In the Testament of Reuben 5.6 (it may have Jewish roots, but it seems likely that it is a Christian document in the form we have it now) the author writes, “Therefore flee fornication, my children, and command your wives and your daughters that they adorn not their heads and their faces; because every woman who acts deceitfully in these things has been reserved for everlasting punishment. For thus they allured the Watched before the flood; and as these continually beheld them, they fell into desire each of the other, and they conceived the act in their mind, and changed themselves into the shape of men, and appeared to them in their congress with their husbands; and the women, having in their minds desire toward their apparitions, gave birth to giants, for the Watchers appeared to them as reaching even unto heaven.”
It is possible that both 2 Pet. 2.4 and Jude 6-7 allude to this interpretation. One may also postulate that 1 Cor. 11.1-16, especially v. 10 is influenced by this legend. When Paul begins to speak of the Spirit-Flesh contrast in his Epistles to the Romans and to the Galatians he does not indicate that his juxtaposition has anything to do with angelic beings corrupting humanity.
In a list compiled by Andrew Louth (Ancient Christian Commentary on Scripture: Old Testament I, 123-124) he quotes Clement of Alexandria and Nemesius of Emesa as also interpreting this passage to be angels
the archives near Emmaus 
I once had a professor who said something like “Evangelicals proudly proclaim that Scripture is the word of God and all of it we are supposed to preach from! Let me ask you, when was the last time you heard a sermon on fallen angels knocking up women?”
To be truthful, for nearly four years now I’ve found the interpretation of it being angels convincing.
One who espouses such an interpretation (and defends it) it Michael Heiser. He has an interesting interview with Greg Boyd. http://www.gregboyd.org/blog/boyd-and-heiser-dialogue-on-the-nephilim-question/
Daniel: It does seem to make the most sense of Gen. 6. It seems that this is part of the apologetic for the flood. There needed to be a way to purge humanity from the corruption that resulted from intermingling with fallen angels. It seems so very absurd which is why I think the Seth/Cain family lines theory is appealing to many.
I will take a look at that Boyd interview.
Brian,
You understate how ubiquitous this view was in the Second Temple period. It’s pretty much the only one. You have to start with the Septuagint whose translation of these verses appears to support an angelic understanding. then go to Enoch–and some scholars propose that the enochic stories go back as far as Genesis or further, and then move into other pseudepigraphal and NT material. Philo, Josephus, the Dead Sea Scrolls, and early Christian writers such as Iranaeus, Justin, Athenagoras, Clement of Alexandria, Tertullian, and (possibly) Origen all believed the sonns of God in Gen 6 to be divine beings who in one form or another procreated with humans.
The first context for an interpretation of Genesis that does not appear to favour the supernaturalists’ view derives from the first century via the Biblical Antiquities of Pseudo-Philo which seems to foreshadow later Targums that interpret בני־האלהים as “sons of the judges.”
This is beyond “strong tradition”, it is the tradition that directly affects many groups in the Second Temple period and almost certainly NT authors. It is all through the literature.
Wow, I had no idea that it was that wide spread. It seems evident that later interpreters introduced the Cain/Seth juxtaposition because they couldn’t make sense of the angelic beings interpretation.
Even creepier, when you read Gen 6:7 it leads you to consider that these fallen “Son’s of God” might have been tapering with the DNA of the entire “breathing or fleshly creation”! Is it possible, that just as Noah was “perfect” in his generations…that the animals that were drawn to the ark were also of pure genetics or DNA? And, even past that, that this tampering with the DNA was what has led to the “birth defects” we see in the breathing creatures and human population today? Seems the ark was possibly a rescue mission far beyond our present day considerations…
@Nancy: It does seem like 6.1-3 were inserted to provide justification for the flood narrative. I don’t know if this means that the animals were also deemed corrupted as was much of humanity, but it is a possibility.