Putting Remote C4 in/on the bunker is an effective last-ditch defense.
Using Gas or Smoke when you storm the bunker greatly increases your odds of success.
Watch out for Snipers, in the Tower, in the area near the Tower, and on the stone arch.
If you are defending the Communications Tower, sometimes it's easier to let the bomb get set if there's only one or two men to defend it. You can then kill them and defuse the bomb at your leisure.
If you are attacking, make sure you buy some kind of explosives to destroy the walls once you've captured the Bunker. Don't waste time running around the trees getting shot at by Snipers.
If you are attacking, and if you can get up beyond the Communications Center quickly enough, you can cover the doorway to the enemy spawn point. One or two men with the right weapons and positioning can effectively contain the enemy to their own spawn point for one or two minutes, plenty of time to complete your mission.
If you are defending
and the Bunker has been taken, a Medic can be extremely useful. Even if the
Bunker has been taken according to the game, you can still defend it and the
bomb for quite a while with someone there to heal your team.