Learn German: Welches Futter kaufen wir heute? - Which food are we buying today?

The ending depends on the gender of the noun and its role in the sentence. Futter is a neuter noun (das Futter), and here it is the direct object being bought, which puts it in the accusative case. For neuter nouns in the accusative case, welch- takes the ending -es.

Since "Welches Futter" is at the beginning of the sentence, is it the subject?

No, the subject is wir (we). In German, question words like welches and the nouns they are attached to must go at the very beginning of the sentence. The verb (kaufen) stays in the second position, which pushes the subject (wir) to the third position.

If we were asking about a masculine noun like "Apfel" (apple) instead, how would the question change?

Because the noun is still the direct object (accusative case), you would need the masculine accusative ending -en. The question would become: Welchen Apfel kaufen wir heute?

Does "Futter" mean the same thing as "Essen"?

Not quite! While both translate to "food" in English, Futter is specifically used for animal feed or pet food. If you are talking about food for humans, you would use Essen. This sentence implies we are shopping for our pets!