Minecraft wiki entry for Farming, associated text: As usual, spiders generally need to be separated or killed off to avoid them blocking other mobs.
The killing chamber must not allow various monsters to aggro:
Creepers can't see you up close, lest they ignite.
The system must not allow baby zombies to escape and run wild. Remember that they can go through a 1-block hole.
Skeletons can't be able to shoot at you.
Naturally, the works need to be enderman-proof, and the areas where you wait should have low ceilings to protect you from any who do show up.