To whom does the phrase "all flesh" refer?
Rashi and Targum Yonasan: Even the animals, beasts and birds who had all taken their cue from man, and were interbreeding. 1
Targum Onkelus and Ramban (in his second explanation): "Kol Basar" refers to the whole of mankind.
Lev Eliyahu (Bereishis p. 34): Why did the animals' actions help bring the Flood? They do not have free choice! [He answers,] through man's sin, Tum'ah and spiritual germs infect the world.
Rashi writes: "The animals would mate with other species." Earlier (Rashi to Bereishis 6:7), however, Rashi gave two explanations as to why the animals were destroyed. The second approach was that they were destroyed because they had been created only to serve man, and not because of their own corruption.
Mizrachi - This Rashi fits only with his first explanation to 6:7, namely that the animals corrupted their own ways. According to the second explanation, however, it was the people who would cross-breed the animals (Sanhedrin 108a).
Gur Aryeh #1: Both explanations concur that the animals would [voluntarily] mate with other species. According to the second opinion, however, this was not the reason that they were destroyed, as they had never been commanded not to do so.
Gur Aryeh #2: After the animals were initially cross-bred by people, the animals continued to do so of their own volition. 1
What is the meaning of the extra phrase, "... and behold it was corrupt (Nish'chasah)," which is immediately followed by, "for all flesh has corrupted (Hishchis) its way... "?
Seforno: It means that, since all flesh had corrupted its way and was guilty of robbery, the world was on the road to self-destruction - even if HaSh-m would not punish them - because such immoral and antisocial behavior would inevitably diminish their ability to have children and would destroy the world's civil structure.
Why does the Torah add the words, "Al ha'Aretz"?
Because it was only the land creatures - humans, animals, beasts, birds and vermin that interbred, but not the fish. 1
As intimated in Rashi. Indeed, the Torah inserts the word "Eretz" over and over again in the current Parshah (some of which the commentaries explain in different ways), implying that the fish did not perish in the Flood
רש"י: נזקקין לשאינן מינן: קשה שבסוף פר' בראשית פירש רש"י בפירוש ב' שבעלי החיים נמחו כי הם נבראו בשביל האדם, ולא בגלל שהם השחיתו את דרכם?
רא"ם: רש"י כאן כפירושו הראשון שם שגם בעלי החיים השחיתו את דרכם, ולפי הפירוש השני שם צ"ל שהשחית כל בשר את דרכו כי האדם היה מרביע מין על שאינו מינו ככתוב בגמ' בסנהדרין (דף קח.)
גור אריה: לשני הפרושים שם היו בעלי החיים נזקקים לשאינם מינם, אלא שלפרוש השני לא זו הסיבה שנמחו שהרי לא נצטוו, אלא מחמת חטא האדם.
גור אריה: תחילה הרביע אותם האדם ואחר שהורגלו בזה עשו כך מעצמם, ולכן נאמר "כי השחית כל בשר את דרכו". עיי"ש. 1
הגור אריה התקשה למה רש"י מפרש כמדרש שהחיות השחיתו דרכם, ולא כגמ' שהאדם הרביע מין על שאינו מינו, ולכן ביאר הגור אריה שהאדם הרגיל את החיות, [ואין מחלוקת בין המדרש לגמ'].