Well, when Paulo was hiding his jewels and Ben and Juliette came in, Juliette said that Tom had been in the pearl a few days earlier. I think it's because he has a thing for Jack. he had an 'uncomfy' moment with him during ben's surgery. "I'm Tom, by the way", Jack just ignores the comment. I believe Tom was spying on Jack, like a webcam, you know, watching him wash dishes, push buttons, all sensual things no doubt.
Boone may be gay, but I believe Tom IS gay. If I'm not mistaken, he did a happy dance when Locke blew up the sub.