The checkered flag signifies the end of the race. It also just symbolizes racing in general.
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The green flag simply indicates everything is fine. Spotters at each fence will wave a green flag if a horse falls, and the horse & jockey both recover.
A green flag signifies the start of a race in auto racing. It can also signify the end of a caution period on the track or that the entrance to the pit stop is open.
The Libyan Flag under Muammar Qadhafi was exclusively green. I am unaware of other green flags.
Green flags are used in various sports to indicate all clear or it is safe to proceed.