My Wild Tom Bombadil Theory
Melkor was likely the very first being created by Eru, and he poured much of his power into Middle Earth. He was also deemed necessary by Eru for Arda to reach it's true potential, and therefore cannot be wholly evil.
Melkor certainly wanted to taint Middle Earth with his power, and thus he was pouring an evil and corrupting power into it, but perhaps the process of creating such power required him to separate out the good from the raw power he had inside him?
Could Tom Bombadil be the manifestation of Melkor's good side, shed by Melkor in his process of becoming Morgoth and poisoning Middle Earth? It would explain why Tom was first and why he is utterly innocent.
Perhaps it would explain why it would be so difficult (but not impossible) for Sauron to defeat Tom, as is suggested during the council of Elrond. If Morgoth kept all his 'combat magic' type power, and separated only the power to heal/preserve/endure, then Tom, while extremely difficult to dominate, would have no actual way of fighting or harming Sauron, in the end Sauron would likely be cunning enough to find a way to win because he is the only one who can cause damage to the other, despite being the weaker of the two beings.