Swift's masterwork is a classic satire, full of social, political, and philosophical commentary both overt and subtle. Most readers are familiar with Gulliver's first two travels, as a giant among the tiny Lilliputians and a living doll among the titanic Brobdingnagians (so familiar, in fact, that both races have been immortalized as adjectives describing their relative sizes). These two adventures are visually vivid, their contrasts simple to grasp. Gulliver is at his youngest, most optimistic, and most forgiving, and these tales translate readily and often to fare for children and casual readers. It's what I think of when I think of Gulliver, too.
The third and fourth voyages, to Laputa (and its neighbors) and the land of the Houyhnhnms, are far darker and less obvious in their critiques of man. The early voyages make fun of the vapidity and scurrilousness of politicians and government, and who doesn't enjoy that? But the later voyages explore man's baser natures, our violence and brutality and coarseness. Here Swift engages in a refutation of the Enlightenment itself, questioning a slavish devotion to science, even, as a churchman, he mocks petty differences between faiths. Taken as a whole, Gulliver's travels are a scathing indictment of 18th-century English life, of inequality and so-called progress.
Gulliver himself, presented as the everyman common in the travel tales so popular then (Robinson Crusoe was less than a decade old), starts out as a wide-eyed wanderer with notions of honesty and the goodness of men. By the end he is disgusted by what he has seen, his faith in humanity worn away, leaving him cynical and reclusive. That evolution was intentional on Swift's part, an unsubtle warning that knowledge and experience may bring darkness rather than enlightenment.