My favorite fruit is ...

My favorite fruits are ...

Sorry, I was going to add an edit:

... is the apple

... are apples and pears (e.g. because "fruits" means different types).

But mikefm's version does sound more natural.

My favourite fruit is apples. (“My favourite fruit” is the subject of this sentence.)

 

If I may quote myself on this matter:

My favourite fruit is apples

My favourite fruits are apples (correct but sounds wrong!)

My favourite fruits are apples and pears

Re #5

I would dispute the 'correctness' of version no. 2. 'Fruits' in the plural, unless used metaphorically ('the fruits of all his efforts'), means 'different kinds of fruit'. So while the sentence may be grammatically correct, it is semantically incoherent (which is doubtless why it 'sounds wrong').

While I think what I've just said is right, it can lead to difficulties, and to perfectly logical sentences which cannot be put into English. For example: 'The apple tree was weighed down with hundreds of fr...' You are pretty well forced to recast this as either 'The tree was weighed down with hundreds of apples' or 'The apple tree was weighed down with masses of fruit'.