Well, i know that the 'orange' part comes from the indonesian word 'orang' which means person. And in this novel, they were trying to make a respectale man out of .. can't remember his name. In other words, they were trying to get him to be good without having to consciously think of being good, so that he'd run like 'clockwork'.
So, an' orang' that goes off like clockwork - a clockwork orange.
Badly explained, but i'm tired.