"My favorite fruit is THE apple." or "My favorite food is simply AN apple." Apple alone - without "the" sounds like a type of taste (a descriptive word rather than a proper noun.) "Apple is my favorite kind of pie' or 'when it comes to candy, my favorite is apple." Finally, "are apples" could be made correct in this way: "My favorite things to eat are apples." In this sentence, we have a plural object (pronoun things) and a plural auxiliary verb (are). Notice in your sentence, you have food (singular) and are (plural)... and yes apples (plural). Try to keep it consistent with the subject rather than the object. With a little study, you will quickly lean to see the difference. Food - is - apples - OK Food - is - an apple - OK Food - are - apples - not so ok

Sometimes nouns are group nouns, meaning the word looks like a plural, but in grammar is treated as singular. This does sound strange to the ear of a native speaker, and I personally try to avoid such situations by using alternate phrases. In this case, instead of saying "my favorite food is apples", I might say "the apple is my favorite food". Both are correct.

Both of those would sound awkward to a native English speaker. The best option would be to rearrange the sentence into "Apples are my favorite food". I understand that this could get very confusing for some, because it would still be okay with certain foods like "My favorite food is pie" = Good "My favorite food is apple" = Bad

Alex's answer is really clear and helpful. You've asked a good question and this is also a tricky thing for native speakers, which is why we would usually say "Apples are my favorite food."