The fact that there are so many different RPG's that use their elements in so many different ways really makes you question the actual value of the elements. In actuality, there are only four solid elements, Earth, Fire, Water, and Air, but through widespread use these elements become broken down into their lesser factors. The gameplay of an RPG has alot to do with the method used to activate it's elements, I thought it was pretty sweet in FF7 the way they used the effectiveness of elements on non-elemential enemies, such as electricity hurts machines, fire hurts animals, and gravity hurts dragons. And in Chrono Cross they had the thing up in the corner that made elemential moves stronger when more of it was lit up in it's color. And then there's always pokemon, which is almost completely based on elements.

Here's what elements I think are most best paired together

Red (Fire, Heat)
Blue (Water, Ice)

Brown (Earth, Rock, Ground)
Yellow (Air, Lightning, Wind)

Green (Nature, Plant, Grass)
Purple (Poison, Status effects)

White (Light, Holy)
Black (Dark, Undead)