A Good War Base

1. Protect town hall. Your town hall is one star by itself and can be the only difference between a 3 and 2 star attack.
2. Center your clan castle. Your reinforcements will be more affective if they are in the midst of your defenses.
3. Storage does not matter. During war they are not stealing from you but the war bonus loot, so you can safely place your storage outside walls.
4. Encircle your main defenses. Put a box of wall around your best defenses, so they are hard to get.

Loot Chaser has its top 10 tips for wars in general.

Of course that is just the basics, so check out this more advanced design.