As Anthony Burgess writes in the introduction (entitled "A Clockwork Orange Resucked," hee hee) the title refers to a person who "has the appearance of an organism lovely with colour and juice but is in fact only a clockwork toy to be wound up by God or the Devil or (since this is increasingly replacing both) the Almighty State."
In other words it stands for the "application of a mechanistic morality to a living organism oozing with juice and sweetness." So, basically, it refers to a person who is robotic behaviorally but one that is, in all other respects, human. The title is significant not only because Burgess references it about, oh, a dozen times throughout the book, but also because it sums up what threatens our protagonist-narrator.