What do you think 'it' refers to in stanza 3?

"A Poison Tree" is a poem by William Blake about the dangers of resentment, with wrath imagined as a seed which then, because of the way it is treated by the speaker, grows into a tree. In the second stanza, then, we can assume that "it" refers to this wrath; if we look back at the first stanza, this is a logical continuation of "it" in the final line, which represents a wrath which grew because the speaker did not express it.
The second stanza describes the process of this seed of wrath growing as the speaker "waterd" it with "fears," "tears," and "smiles"—that is, encouraging the wrath to grow with everything he does. By the time we see the tree in the third stanza, it has grown "till it bore an apple bright," the wrath here having been fed to the point that it is able to produce something visible to indicate to the "foe" that it exists. Blake is suggesting here that wrath untold will always be revealed eventually simply because nurturing it in silence only makes it stronger, so it would be simpler just to tell the wrath in the first place to make it quickly "end."