What is that which drew from out the boundless deep that now turns again home in "Crossing the Bar"?

In the literal interpretation of the poem, this refers to the tide. The preceding two lines also refer to the tide, noting that it is "too full for sound and foam." In these lines, the speaker notes that the tide originates in a source of greater power that pushes it in and then pulls it back out. Just as the tide draws its original strength to push forward toward land from this "boundless deep" source (the gravitational interaction between the Earth and moon), it also has a natural inclination to retreat back to this source, creating the never ending rise and fall of the tide.
Metaphorically, the speaker is referencing that his soul wishes to return to the "boundless deep" where it was created. Here, his soul is the "that" in the lines, and "home" is a place of eternal significance. His soul, therefore, longs to return to God, his Pilot, who is referenced through metaphor in the final stanza.