When a ship gets destroyed, it will normally take all of the crew (and Marines) with it. To save this valuable resource, if it looks like a ship is doomed, (badly crippled, or has a dozen drones incoming and no defenses) use Emergency Evacuation to rescue the crew (and the Marines). The ship will still be destroyed, but you'll have more boarding parties on the rescuing ship, which will be useful as marine raid ammunition, if nothing else.

Also, if a ship is in danger of capture, Emergency Evacuation before the end of the turn will prevent any defending Marines from getting killed - while the enemy Marines are stuck on a ship that's going to blow up (after Emergency Evacuation, the ship automatically self-destructs at the end of the turn). If the enemy has already used his available transporters to board the ship, then he will not be able to rescue any of his own Marines.