In a medium sized saucepan, add the water, butter, and salt, and bring to a boil over high heat.
Reduce the heat to medium and add the flour all at once. Stir rapidly. The mixture will form a dough ball that will pull away from the sides of the pan. It helps to use a wooden spoon to stir as the dough will be rather thick. Continue to cook for a couple minutes.
Remove the pan from the heat and let cool for a couple of minutes. Stir so that the dough cools more evenly. You want the dough to be warm, just not so hot that when you start adding eggs they cook as they hit the dough. Add the eggs one at a time, stirring after each addition until the eggs are incorporated into the dough. (Do this part in a mixer if you want, or by hand with a wooden spoon.) The dough should become rather creamy.
Stir in the grated cheese, thyme, and a few grinds of pepper.
Preheat oven to 425°F. Spoon out small balls (about a heaping tablespoon) of the dough onto a Silpat or parchment lined baking sheet, with at least an inch separating the spoonfuls. Place in oven and cook for 10 minutes at 425°F. Lower heat to 350°F and cook for another 15-20 minutes, until puffed up and lightly golden.