This question concerns what is called, technically, concord, or, more generally, agreement. That is, the agreement of subject and verb. So, to take your example (but avoiding fruit for the moment): My favourite animal is the elephant. Here we have concord between the (singular, countable) subject and the verb. We also have agreement between the singular subject and the complement (the elephant). We could equally well say: My favourite animals are elephants. Again concord rules.
In the occasional case where the subject is singular and the complement is plural, the verb agrees with the subject, not the complement. So: My favourite meal is baked beans. Not *My favourite meal are baked beans. (The asterisk is the device traditionally used to show a grammatically unacceptable example). This, by the way, explains My favourite food is noodles, noodles being almost always thought of in the plural.
However, there is another issue involved, and that is the way we use nouns to talk generically, that is, about classes of things. When we say My favourite animals are elephants, we are talking about elephants as a class, rather than any specific and identifiable elephants (in which case we would say My favourite animals are the elephants – e.g. the ones in the zoo). With countable nouns there are three options when talking generically:
An elephant is a mammal.The elephant is a mammal.Elephants are mammals.
With uncountable nouns, there is only one option – the “zero article”:
Carbon is an element.
So far so good. But your example with fruit somewhat complicates things, since fruit has two plural forms: the more common fruit, as in The tree is pretty but its fruit are poisonous. And fruits, as in Mangoes and pineapples are tropical fruits. (The fact that fruit can also be uncountable, as in Fruit is good for you, need not concern us here, since in the context of my favourite fruit we are talking about one fruit among many, and hence making it countable).
Taking all this into account, we now need to explain why the following seem acceptable (and, indeed, are acceptable when you try them out on native speakers):
1. My favourite fruit are apples2. My favourite fruit is apples.
Less likely, but grammatical, are:
3. My favourite fruit is the apple.4. My favourite fruits are apples.
Example 1 is easily explained, since fruit here is the plural form, and hence the example follows the pattern: My favourite animals are elephants.
Example 2 I can only explain as being singular fruit (analogous to My favourite animal…) but that the plural apples is the generic form – a slightly less pompous-sounding way of saying 3. My favourite fruit is the apple. Nevertheless, when questioned about example 2, native speakers feel a bit uncomfortable, recognising it as being somehow deviant, but the best of a bad job. Example 4 might be an attempt to be hypercorrect, with regard to concord, but it is only really likely in cases like My favourite fruits are apples and pears.
If example 2 is acceptable (and I think it is), it raises the question: why can’t we say My favourite animal is elephants? The reason is, I think, that it is not unusual to think of apples, generically, in quantities of more than one, but not elephants. In fact, the smaller you get, the more likely it is you would use a plural:
3) My favourite fruit is cherries.
Compare: My favourite fruit is the cherry
4) My favourite vegetable is peas.
Compare: My favourite vegetable is the pea. My favourite vegetables are peas
This also accounts for your watermelon and pineapple cases, I think. My favourite fruit is watermelons conjures up images of eating several at one sitting. The uncountable, zero article, generic watermelon gets round the concord problem, and conjures up an acceptable image of tucking into a watermelon without necessarily eating it all. But it doesn’t work for apple: *My favourite fruit is apple. Uncountable apple and countable apple are very different items, in the way that uncountable watermelon and countable watermelon are not.
So, as a general rule, I’d say that, when talking generically, the smaller the item, the more likely it is we will pluralise it. (I like cherries). For bigger items, use an uncountable form, if possible. (I like watermelon). If not, let concord rule. (My favourite animals are woolly mammoths). (Author: Scott Thornbury)