Cilia are slender, tube-like projections that extend from the membrane of eukaryotic cells. There are two basic types of cilia: motile and primary. Motile cilia are used for movement. An example would be the motile cilia found lining the windpipe in humans. They help remove dirt and particles from the air passages. Primary cilia are found on most animal cells. They are used not for motion but for chemical sensing on the cell's surface.
Flagella are whip-like appendages that protrude from the cell membrane. Like motile cilia, they are used for locomotion. They are found on eukaryotic and bacterial cells. The main difference between eukaryotic flagella and cilia are related to the motion of the extension. Flagella use a simpler wave-like motion while cilia use more complex strokes. The tail section of sperm cells are an example of flagella in the human body.
Microvilli are also tube-like cellular extensions like cilia and flagella. Microvilli are different, however, in that they are shorter in length and more tightly packed on the surface of cells. They are used not for locomotion, but for absorption and secretion of chemicals in and out of cells. They are effective in this function due to their large collective surface area. An example in the human body would be the lining of the small intestine where microvilli aid in the absorption of nutrients into the bloodstream.