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What exactly is the difference between a recirculation system and a run to waste system?

A recirculation system is one where the nutrient solution is continuously pumped from a reservoir to the plant and then drains back to the reservoir.

The same water is used over and over through the reservoir is occasionally "topped up" to replace the water used by the plant. Flood and drain and NFT (nutrient film technique) are examples.

A run to waste system is where the nutrient solution is periodically pumped from the reservoir to the plant then allowed to drain away and is discarded. Growing in coco peat is an example of a run to waste system.

What is the best medium to use?

There is no best medium. All the media on offer are suitable depending on the system you decide to use.

For recirculation systems you should use an inert medium such as expanded clay, Rockwool, or perlite. For run to waste systems you may use either an inert or organic medium such as coco peat.

Success with any medium comes down to good management.