Batu Cermin Cave is the easiest natural sight from Labuan Bajo, a limestone cave system just outside town. The visit is short but worthwhile: narrow passages, fossil-bearing rock, bats, and shafts of light that explain the "mirror stone" name when conditions are right.
Bring shoes with grip and expect heat outside the cave. Local guides usually provide helmets and lights. It is a good spare-morning activity before an afternoon flight or after returning from a Komodo boat trip.