Mysterious beings?

[Mumriken]

I was wondering if some of you tolkien loremasters could enlighten me about the mysterious beings that lives in arda but whose origins aren't clearly explained. There are so many holes that one could try to patch together using the surrounding fiction. Maybe it will be a bit overwhelming but maybe not. These characters/beings stand out to me while reading Tolkien's works. There might be more of them and if there are please tell:

• Tom Bombadil
• Ungoliant
• Beorn
• Goldberry
• Dead Men of Dunharrow
• Hobbits
• Wraiths

Tom Bombadil doesn't fit in the story at all, and his powers and what little we know about him suggests he is far more powerful than any maia. He was there before the dark lord (Melkor) entered. Weren't the Valas the first to enter arda? It's the same thing with Ungoliant, another very powerful being but not a maia corrupted by Melkor and with a will of it's own. Ungoliant almost seems to be a peer to Melkor. There never was a master, servant relationship between the two as there would have been between Melkor and Sauron. Are Ungoliant and Tom Bombadil of the same "kind"?

Goldberry is less mysterious but still we have no explanation as to what she is. The daughter of the river, this brings in another potential race of beings. (Nature spirits) which Tom Bombadil also maybe could be. But Goldberry and Tom also seem different, I find it hard to believe Tom could be a nature spirit since he was in arda before the valas meaning before nature. Maybe he is the embodiment of arda itself. Though I find it more likely that he and Ungoliant are of the same kind. It's suggested Ungoliant came from the void, maybe Tom also came from the void and therefore necessarily isn't beneath anyone? He has referred to himself as master and fatherless. Maybe that is why the ring has no power over him, because not even Manwe or Melkor has power over him. In the same way as Melkor had no power over Ungoliant?

Beorn is clearly a man yet can turn himself into a bear. It is said that Morgoth bred werewolves and vampires in Utumno. Beorn is a werebear, meaning somehow he should be able to trace his origins back to Morgoth's experiments. However, I'm not really sure but had men awaken when Morgoth carried out his experiments and created the trolls and orcs and all the wicked creatures? So how could Beorn be a man and a bear if there were no men back then only elves. I don't remember what morgoth did to men when they woke. Could Beorn's ancestors be one of the men that were seduced to Morgoth's side and then destroyed in the war of wrath...and Beorn is the last living werebear?

It's clearly explained what the dead men of the dunharrow are, yet I'm not sure how they could be what they are? How could a mere man like isildur curse an army making it unable for them to go to the halls of mandos or wherever men are going after they die. I don't understand ghosts in general, what exactly are the wraiths in the barrow downs and the dead spirits in the marshes outside mordor. What keeps them from passing from the world? Wraiths and the men of dunharrow go hand in hand. It's the big why are they ghosts question I wonder about. Actually I think we could squeeze in orcs here as well. Orcs are tormented elves, so where do they do after they die? Are wraiths the spirits of orcs?

And last the hobbits, a new race? How did this race come about? They are short like the dwarves, maybe they are a crossbreed between dwarves and men? If this is the case, where would hobbits go after they die? A lot of questions I'm sure you could help me answer them.