[Inziladun]

My first reading of LOTR was too long ago for me to recall how I felt about Bombadil then.
Now, however, he comes across as an enigma, yes, but a comforting one nonetheless.
It's obvious his concerns are different from any other character we meet; he's doing something that feels important, but it's a mystery to all but himself (and maybe Gandalf).
I see Tom in fact as the anti-Gandalf. The wizard is totally wrapped up in the fate of Middle-earth: he's focused on Sauron, and all that he does is a reflection of that.
Tom is apparently more of a "big picture" guy. He's got his own agenda to take care of, but it's so diffuse that he has a lot of leeway in how he can accomplish it.
Gandalf himself made the "opposites" observation when he called himself a rolling stone, and Tom a moss-gatherer.
Although the reader is given only the bare-bones about Tom and his nature, I never get any feeling of ill-will from him. Like Pitch said, he even treats Old Man Willow with respect, allowing him his own part in the Forest, but merely bringing him to heel when he crosses the line.
Same thing for the Barrow-wights. Tom banishes the one that had taken the Hobbits, but he doesn't turn all of them out. He recognizes that helping Frodo is something he's meant to do, and does it. He's obviously Good; his means of doing good works are just more obscure.