"The plate is on the table" - this is normal usage for "on". "on top of" has a similar meaning, but is usually used for something higher up. Especially things which are out of sight or very high. Such as "The box is on top of the shelf", or "The house is on top of the hill". "Above" usually means flying or floating - "The clouds are above the mountain". But it can also be used when comparing "above" and "below", such as "The leaves of the plant are above the ground, but the roots are below" or "The submarine is above the water, but it can go below".