What is the satire in Gulliver's Travels?

Gulliver's Travels is a satirical work, and its main target is the experimental science promoted by Enlightenment thinkers such as Sir Isaac Newton. 
The Enlightenment was marked by a particular theory of human nature, wherein human beings were seen as inherently rational creatures who were capable of attaining intellectual enlightenment; a certain optimism marks many writings from this time period. Swift, on the other hand, displays a pessimism about human nature and rationality that runs counter to the spirit of the Enlightenment. The strongest satire concerning human nature can be found in part IV ("Voyage to the Country of the Houyhnhnms") where humans are like the irrational Yahoos.
His first adventure into Lilliput is a satire about the wars fought between England and France, with Blefescu standing for France and Lilliput for England. In general, the first two parts satirize European politics of the time, and George Orwell believed that Swift's attacks were targeted at the Whig Party. One can find an eviscerating criticism of England in this speech uttered by the King of Brobdingnag:

My little friend Grildrig, you have made a most admirable panegyric upon your country; you have clearly proved that ignorance, idleness vice may sometimes be the only ingredients for qualifying a legislator; that laws are best explained, interpreted, and applied by those whose interests and abilities lie in perverting them ... I am dwell disposed to hope you may hitherto have escaped many vices of your country. But by what I have gathered from your own relation ... I cannot but conclude the bulk of your natives to be the most pernicious race of little odious vermin that ever suffered to crawl upon the surface of the earth (II.vi).

The satire is first directed at England, at European politics in general and then, as the book progresses, it is directed at human nature itself.