Bunkers are treated exactly like an immobile vehicle with an Armour Value of 13 all rounds when shot at or assaulted. Troops inside a bunker may shoot as if they were being transported in a vehicle, i.e. half of them may fire and they may not be targeted separately. However, troops on top of the bunker do count as a separate target from the bunker although they will usually be able to hide behind a wall or parapet (getting a 4+ cover save). Use common sense in regards to bunker capacity (generally 10 models is a reasonable number for a normal bunker) and entrance/exit points usually being a modelled door.
Bunkers
Source: 3rd-A-Palooza (3.5) Rulebook v1.4, p. 59