Why was the large stone placed on top of the well?
Rashbam: Either so that nobody should fall in, or so that nobody should steal the water.
Ha'Emek Davar: It was lest people fall in, or lest the water impair witchcraft (refer to 29:2:153:3*).
Why were the three flocks of sheep crouching next to the local well?
Rashi (Pasuk 3): Because it required the combined strength of all the shepherds to roll the stone from off the well (they were waiting for the others).
Why does the Torah see fit to record this episode?
Ramban #1 and Rashbam: To teach us the immense strength of Yakov Avinu
Yakov's strength will be revealed again when he fights with the angel (in Parshas Vayishlach).
To which the well hints.
Since Torah is compared to water.
Bear in mind that Yisrael are also compared to sheep, as we mention every Friday night in "Lechu Neranenah".
See also Ba'al ha'Turim.
What does "Hinei" mean?
Tosfos ha'Shalem (3): It is something that was not known until now, e.g. "va'Boker v'Hinei Hi Leah." (He only saw the well now.)
Ha'Emek Davar: It says Hinei a second time for a second Chidush (in addition to seeing the well itself)
Why did Yakov go to the well?
Tosfos ha'Shalem (3): He learned from Eliezer, who went to the well to ask about matters of the city, if he will be accepted as a guest. Also, Rivkah told him 'go to the well - just like Eliezer found me there, if you find a daughter of Lavan there beautiful like myself, she is proper for you.'
Why does it say "the large rock"? It was not mentioned before!
Ohr ha'Chayim: This teaches that it was exceptionally big.
Malbim: It hints to the Yetzer ha'Ra. It covers the well (salvation). When all the flocks gather (Yisrael are united), it is removed, and Hashem's influence is opened. 1
Ha'Emek Davar: It was normal to cover wells, lest people fall in, or lest the water impair witchcraft. 2
Malbim: However, each time Yisrael returned to sin
Why does it say "veha'Even Gedolah", and not 'ha'Gedolah'?
Ha'Emek Davar: It was wide and thin. It was big (too hard for a person to move it) only "Al Pi ha'Be'er", but not when it was next to the well.