Genesis 6 – Skeptic's Annotated Bible answered

The phrase “sons of God” means here those of the seed of Sem who followed God. But even they left their former ways. So they were not angels, and angels do not have a body, and can therefore not have sex.
The author of the SAB claims that “There seems to be no good answer to [who the sons of God were].” Which is utter nonsense. If he had just consulted a single commentary, he would have found it. Let me just quote John Gill, which I use most often in my rebuttal as it is already hundreds of years old, freely available, and considered to be among the most eminent commentaries:

those "sons of God" were not angels either good or bad, as many have thought, since they are incorporeal beings, and cannot be affected with fleshly lusts, or marry and be given in marriage, or generate and be generated; ...; but rather this is to be understood of the posterity of Seth, who from the times of Enos, when then began to be called by the name of the Lord, chapter 4:25 had the title of the sons of God, in distinction from the children of men; these claimed the privilege of divine adoption, and professed to be born of God, and partakers of his grace, and pretended to worship him according to his will, so far as revealed to them, and to fear and serve and glorify him.

The author of the SAB misunderstood this verse. It's not about shortening life spans, that was probably the result of the genetic bottleneck humans went through after The Flood and when longevity genes were lost. The 120 years here refer to the total time remaining before The Flood.
On how long the human life span is, see Psalm 90:10.

In this verse giants could refer to stature, but more probably it refers to their great wickedness, cruelty and tyrannic oppression.

As the whole earth was filled with man's evil, God destroyed it to show what sin deserved, to show his might and his righteous punishment that will come upon evil. It was a singular warning for those who came after. But also, as man's heart was evil, God showed his mercy in not destroying it a second time. God's mercy and righteous punishment are not opposing attributes, both glorify him, and both will be seen so very clearly on the Last Day, the Day of Judgement.

The phrase “God repented” is used in the Bible when God changes his actions. The meaning of it is explained very well by John Calvin:

The repentance which is here ascribed to God does not properly belong to him, but has reference to our understanding of him. For since we cannot comprehend him as he is, it is necessary that, for our sakes he should, in a certain sense, transform himself. That repentance cannot take place in God, easily appears from this single considerations that nothing happens which is by him unexpected or unforeseen. The same reasoning, and remark, applies to what follows, that God was affected with grief. Certainly God is not sorrowful or sad; but remains forever like himself in his celestial and happy repose: yet, because it could not otherwise be known how great is God's hatred and detestation of sin, therefore the Spirit accommodates himself to our capacity. Wherefore, there is no need for us to involve ourselves in thorny and difficult questions, when it is obvious to what end these words of repentance and grief are applied; namely, to teach us, that from the time when man was so greatly corrupted, God would not reckon him among his creatures; as if he would say, 'This is not my workmanship; this is not that man who was formed in my image, and whom I had adorned with such excellent gifts: I do not deign now to acknowledge this degenerate and defiled creature as mine.' Similar to this is what he says, in the second place, concerning grief; that God was so offended by the atrocious wickedness of men, as if they had wounded his heart with mortal grief: There is here, therefore, an unexpressed antithesis between that upright nature which had been created by God, and that corruption which sprung from sin. Meanwhile, unless we wish to provoke God, and to put him to grief, let us learn to abhor and to flee from sin.

God is the judge of all mankind. And his judgements are righteous.

Why did the author of the SAB display a thumbs up (Titus 3:1) for “speak evil of no man,” but here he wastes no time to slander Noah?
First of all, Noah wasn't drunk in front of his sons. He was in his own tent, and undressed and went to sleep. Secondly, it's unknown if he knew of the effects of wine in this manner or not.
On the meaning of perfect, see Matthew 1:19.

So every judge who orders punishment for someone found guilty is now committing violence?

The author of the SAB makes various claims about the Ark:

1. It's length was indeed 450 feet (about 135 metres).
2. The ark was too big to be seaworthy. That is false. See the stress analysis results.
3. Their are many accounts of ships, build from wood, that were at least this big, carrying 3,000 people for example.
4. The author of the SAB has found some weird info on the creationwiki site. Something about a 5:3 ratio. That information is no longer there, but this creationwiki site contains an incredible amount of faith in hoaxes, and should be avoided by anyone interested in the truth, so it could well have been there.
   On the dimensions, it may be interesting to note that the dimensions of the ark are optimal for its purpose, see section Ark Shape. Due to its dimension the ark could withstand waves over 30 metre! In contrast the ark described in the Gilgamesh flood story is not seaworthy.
5. On ventilation and other scientific questions, see Noah's Ark: a feasibility study.

The author of the SAB thinks it is unjust that all on the earth had to die. But God is the judge of all. Somehow the earth had become so filthy and so corrupted, that all men had to die. The beasts of the field had to die to in this process. But God was their creator, he gave them life, could he not take it again? We grant our creators full control over their creations. But the blame was upon mankind as those innocent beasts suffer because of sin brought into this world by man.

This verse contains a short summary and indicated to Noah approximately how many partitions he had to make. Of every species, at least two would enter. It is unsure if this summary simply leaves out the distinction between clean and unclean or if God refined his commandment later. I suspect the former, but in any case if in chapter 7:2 God refines the commandment, there is still no contradiction. As LookingUntoJesus perceived, there is also no contradiction with chapter 7:9 as that verse simply describes the manner in which the beasts went into the Ark: in orderly fashion, two by two. That verse isn't about the distinction or how many of each species went into the Ark.

The author of the SAB scoffs. Is that because Noah could not take enough food? That is quite unlikely. For example, if Noah had to take reptiles, he could have taken either the eggs or the very young, and so for the other species. Also, it's a mistake to believe that supposed predators need to eat flesh. Eating flesh came only after The Fall. For example lions (if they already existed at that time) can eat hay perfectly fine. Besides hay, milk producing animals could have provided food for others. Some animals can hibernate. Again, see Noah's Ark: a feasibility study for more details.