Good vs. Evil
As this is a tale about a deal with the devil, the theme of good versus evil naturally comes into play. The story suggests that greed and hypocrisy are the root of evil, and from Tom's fate it is clear that these do not go unpunished. However, this story also implies that this fate is avoidable: with a set of proper values and sound judgment, people can live "good" lives, combat evil, and evade the devil as Tom was unable to do.
Moral Decay
Though Tom's morals are certainly not in the right place at the beginning of the story, they continue to decay as time goes on, until eventually Tom has become so immoral that he is akin to the devil himself. At first, Tom is reluctant to agree to Old Scratch's terms, even though money is involved. Slowly but surely, though, Old Scratch chips away at his morality until it has decayed completely, and he can look a poor man in the face, whom he has bled out of money, and claim he has not made a cent off of him.
Temptation
In most stories involving the devil, the devil incarnate represents temptation; this one is no different. Tom's interactions with Old Scratch illustrate just how disastrous temptation can be, and they warn readers to be extremely cautious before giving themselves over to it. It is a show of strength to be able to resist desire in favor of what is right; Tom was weak, and he paid the price.