Many possible answers. Dragons (of which there are several kinds), Trolls, Ents, Entwives, even Fell Beasts if you want to use the annoying Peter-Jackson-influenced term.
Hell, the wording for one of the higher level class features of the ~ Dragon Disciple implies that your character actually becomes GENETICALLY half-dragon at a certain level (though at least one dragon in your lineage is a requirement for the class).
Reading the Draconomicon supplement, I got the impression that dragons, especially the evil ones, were some horny SOBs.
Say you’re a dragon. You’re big, bad, and super-intelligent. Don’t you think that there’d be some stigma against changing forms and banging whatever being is around? I don’t want to call it bestiality, but if the shoe fits…
At least with the humanoids, you’re mostly the same. Sure Haflings/Hobbits are kinda small, Elves live way longer than you, and Orcs are… Well, you’ve got to be pretty damn drunk to sleep with one of those things.
To tie this into Tolkien a bit more, I’m fairly certain that Saruman was breeding Orcs and humans, though I don’t think this was the origin of the Uruk-Hai. I could be wrong, though, and I don’t have the books handy, so feel free to step in and correct me.
This is tricky. It appears that Saruman bred humans and orcs to make his large soldiers, his Uruks.
However, Sauron separately had a breed of Uruk-Hai that appeared to be fully orc and first appeared over 500 years before the War of the Ring and helped to conquer Ithilien and Osgiliath.
Yes, entirely fictional. Hobbits were invented by JRR Tolkien and have never existed. Homo floresiensis did exist and shared no particular qualities with the fictional species of hobbits except height, which is not unique to them. There are hobbit-sized people today, have been many hobbit-sized people throughout history, and the only reason anyone calls this particular hobbit-sized people “hobbits” is that the Lord of the Rings movies happened to be in the public eye when they were discovered.
I always got the impression the Metallics were more likely to go for humanoids. Or, maybe it’s just the fact that it’s easier for them, given they have the ability to use Polymorph inborn, rather than just gaining access to it as a spell.
Keeping with D&D, it’s likely that all the Humanoids are potentially, at least, able to interbreed, though only Elf/Human and Orc/Human crossbreeds are specifically mentioned. Giants are also canonically able to interbreed with humanoids. (Half-Giants, Half-Ogres, Half-Trolls and the Orc/Ogre crossbreed I can’t remember the name of.)
The other major half-breeds - half-Dragons, half-Fiends, half-Celestials - involve one highly magical species. (Half-Golems and Half-Illithids, the standard ‘WTF’ half-breeds, aren’t really half-breeds - Half-Golems are magical cyborgs, Half-Illithids are a result of standard Illithid reproduction gone bizarrely wrong.)
Going to LotR…well, that’s already been mentioned.