With respect to modern times, what did the Enlightenment change the most: government, science, human rights, or religion?
While humanity made massive gains in all of these categories, in my opinion the Enlightenment benefited science most. The Enlightenment was a period in history where people looked to reason to explain events rather than relying on supernatural or spiritual explanations. During the Enlightenment, thinkers like Isaac Newton began to use scientific and mathematical principles to describe gravity. This had ramifications in engineering and even military science. Calculus was soon developed to explain scientific principles.
Biology also made great gains during the period. While the Catholic Church frowned upon it, doctors would recruit people who would dig up cadavers for dissection. This emphasis on looking for causes led to the study of anatomy and a better understanding of how the body works. While the old theory of fluid imbalance held sway in medical theory for quite a long time, medical science was improved through the study of bodies.
Although one could make an argument that mankind's views on government and religion changed the most during this period, it is hard to imagine civilization's improvement without scientific achievements.