The red covers were originally there to show that the engine meant business.

The green covers came about because the engineers at Cosworth were instructed to add emission controls to the engine, and they wanted to poke fun at the whole 'green' (global warming, etc) fad. Who wants a performance engine that's restricted?

The blue covers came about because they'd used all the other colour combinations on other heads that they were building for other customers.

Not sure about the black/silver combination - think this was a Ford thing to show that the engine had 'evolved' with EEC-IV.