Rainfall patterns are determined partly by the prevailing wind, which blows eastward and simulates real-life rain shadows.
Planetary Orbit determines oceanic rainfall. It has little to no effect on inland squares. It is is weighted strongly toward the equator, where the oceans are warmer. Increasing this value will tend to cause a thicker band of green vegetation on tropical islands.
Determines how much sea is available, natch. (Extra info on proportion of trenches to shelves needed.)
Determines not only the rockiness of squares but the actual elevation map used. On maps with the smallest ocean coverage setting, this makes a tremendous difference in the amount of total water available. Maps with minimal erosion and ocean coverage will be largely inland.
Native Life Forms
Determines initial xenofungus coverage, but is also used to assess Eco-damage and native spawn rate post-generation.
Cloud Cover has a more global effect, and is cumulative with rainfall from Planetary Orbit. It is responsible for spontaneous generation of vegetation in continental lowlands. In particular, it changes the amount of vegetation downwind from rivers drastically.