The Fill Grid tool, which was introduced in Blender 2.68 works wonders for quickly filling large patches of polygons. It is particularly useful for capping cylinders and for quickly filling gaps during the retopology process.
You can use Grid Fill by selecting two border edgeloops of a whole and then running Grid Fill from the Faces menu (CTRL+F). In order for Grid Fill to work, each of the selected loops must have the same vertex count. In addition, the two connecting edge loops must also have the same vertex count.