I think Atlas Shrugged might qualify -- it takes place in an alternative universe and deals with the implications of a couple of fictional technologies (Rearden metal and John Galt's engine). Animal Farm is really pushing the definition, though.
Since I'm sure everybody's idea of the best three will differ, a list of 32 with summaries so you can pick out the three (out of those which you haven't read) which are likely to appeal to you is probably more useful.