We are stepping on thin ice here.
The fact that there are isolated cases of hybrids doesn't necessarily means that two different species are compatible for breeding.
In the evolution of species, it's been observed that there've been moments in evolution chain where two different species started to breed together, giving birth to a third different evolved specie. Of course, before this happens as something normal, there are strange isolated cases much time before.
And things get messier when you add to the mix magic and fantasy.
On the canon novels are there two documented cases of half-giants, and one of half-goblins. Although no one seems to feel amazed by Hagrid, we can supose that's more common to see a half-giant than we see in the novels.
Those cases, however, doesn't mean that two races are compatible for breeding. The product of such unions must be much more usual and a lot more of half breeds should exist to us being able to determine that both races are compatible.
While cross breeds are strange and few we only can consider them as mutants. Maybe in the far future, evolution turns this mutants into a new specie, but not today.
Applying to this reasoning, I'll say that House Elves are not compatible for breeding, as in the observable environment (canon books) we haven't seen any case of a half-breed, and even if this half-breed in fact existed, it's rarity only can be determined as a mutation (on the contrary, there would be plenty of half-breeds in the wild).