Been thinking about this one for a while - who hasn't? But it's clear to me now that Tom Bombadil is actually Eru Iluvatar, Creator of All.
Surely this theory has been brought up before, but I'm hoping that my tack is somewhat different (in the interest of full disclosure note that I did not go back and read each and every post on each and every 'Who's Bombadil' thread).
Tom's Eru. Tom is named Oldest, Fatherless. Goldberry simply states that, "He is." If that's not definitive, I'm not sure what is. But you know all of these arguments by heart. You probably have all of the counters memorized as well.
But he's not exactly Eru either, in the sense of being a God as we may think of it. It is actually Eru playing the part of Tom (and I think, even Goldberry, as such a god need not be limited, but see more below). I'm not sure if Eru as Tom even knows that he is the God of all at all. This may be due to the God self-limiting itself, almost like a self-induced lobotomy. Or, maybe Eru has gone what we would call insane, and so has set the world on auto pilot and has mentally retreated into the being that is Tom. Running the universe surely has its down days, and maybe Eru got so bored that It decided to go native, as that would be more fun, especially if It could somehow fool itself into playing at being a being like Tom. I would not limit the abilities of a god to not be able to pull off such a deception.
What got me a little down this path was remembering reading
John Varley's Gaea Trilogy where the god of a world goes insane. Also, as Tolkien was a Christian, he read of Jesus, who was the God-Man. Jesus, during His earthly ministry, divested Himself of His God nature (or something like that - I'm not exactly sure how to best describe it, and note I mean no disrespect in any of these Christian comparisons) so that He could be like us (though still God). Whereas Jesus appeared as a human, I think that Tom appeared like those with whom he visited, which is why the Hobbits see him much like a large Hobbit than as a Man or Dwarf. His house is just a little too ready to receive four Hobbits for me not to suspect that he wasn't altering reality to fit the situation at hand. Had Elrond showed up, I get this feeling that the inners of the house would be a little different, and Tom might have appeared differently as well.
Also, in Christianity there is the concept of the Trinity, the Triune God. Not that it's easy to define, but as I understand this, there is one god, but three distinct beings in that godhood. Not three gods, nor three faces of one god. One god that can communicate with the other 'parts,' though they remain one, but distinct.
And so why not have Eru as a similar triune god? It could then express itself as male in Tom, female in Goldberry, and even nature in Lumpkin. How better to see how the theme played out than to plant oneself in the middle of Middle Earth, and then be able to relate to the characters within, whether sentient being, animal/plant, or element?
Anyway, that's my poorly worded take on Tom.