The precise meaning of the title is up for hot debate (nothing hotter than a literary debate), although it touches upon many of the book’s important themes.
There are two primary points in the novel that reference the title. Check 'em out:
The time was past for asking the white folks what to look for through that door. Six eyes were questioning God. (18.30)
They seemed to be staring at the dark, but their eyes were watching God. (18.39)
These two quotes hint that the title relates to the theme of race. In the first quote, Hurston in many ways accuses blacks of looking to whites to learn what their futures hold. The black community questions God only after they realize that white people can’t give them the answer. This seems to be a bad move; by following what the white people have been doing—hanging around the Everglades when a hurricane is coming, for example—the blacks have been led into danger and suffering.
In the second quote, the black people seem to be looking at darkness—perhaps looking beyond race, because everyone is the same when the lights are out. However, though they seem to be looking at "the dark," they're actually looking at—rather than questioning—God.
This switch from questioning to watching potentially means two things. The people could have gained faith in God. Alternatively, they may no longer be asking what their futures hold but watching to see what God will bring.
Why make this the title of the whole book? Good question.
The title is cryptic, but it could mean that the book is about racial and personal independence—not following what others tell you your future holds but instead following God. Janie seems to do just that. She rejects other people's ideas of what she should want in life.
Most of the black characters’ notions of what they should desire seem born out of the still-recent history of slavery. Nanny, in particular, as a former slave envisions that the best possible life is to live like a wealthy white woman, with nice material belongings and plenty of leisure time. Nanny looked to whites to determine what her future should hold and was led astray. Janie, however, goes after what she wants in life: love. We could see Janie as having eyes watching God, rather than watching other people.
The title can also be looked at from the slave/master standpoint. In the first quote, the blacks have realized that looking to the former slave masters, the white people, won’t do. So, they look to the "Ole Massa" (18.29), or God.
This has several implications. Firstly, that God is the master of everyone—black and white—which is an equalizing notion. The second implies that God is the master and that all humans are slaves. As slaves, free will is irrelevant or non-existent. It seems that people's futures are determined by fate or God.
This point is further driven home by nature and the agricultural imagery found throughout the novel. Tea Cake, Janie, and their Everglades friends are all agricultural workers—essentially, people that manipulate nature to do their bidding. By looking at agriculture, man seems to have much control over nature and fate. However, God shows up and can manipulate nature to a much larger degree, coming with a hurricane and flood waters. God makes it clear who the boss really is and who can actually control nature and fate.
In the context of the entire book, the title would seem to mean that individual free will is irrelevant...only fate or God’s will matters. Looking at the second quote again, the people are looking into the darkness; their fate is not illuminated, so they look to God because only He knows what will befall them.
In this light—or should we say darkness?—the title implies that nothing is earned by Janie in the book: her happiness and sorrow is all God’s doing. Her eyes then look to God, wondering what he'll bring into her life next.