fruit/s

Pretty much any of them. Fruit is one of those peculiar nouns that can be either singular or plural or both simultaneously.

Because you are only giving two choices of fruit, then your first sentence would be the correct one. You are asking which fruit is your favorite, an apple or an orange.

Fruit has a generic sense: oranges, apples, bananas, kiwis are all kinds of fruit, and if I had a tonne (1000 kg) of each of these in a 4 tonne truck, I might well say that it was full of fruit.

Fruits refers to the individual items of fruit in a specific way. I threw ten oranges at a hole in the fence, and three fruits passed through.

Which is your favourite fruit, an apple or an orange? - yes

Which are your favourite fruit, apples or oranges? - yes

(To an artist) Which are your favourite fruits for painting, apples or oranges?

Also, what do I answer if my favourite fruit is a banana?

Surely you meant "What is your preferred fruit, an apple or an orange?"