It is an absolute guarantee that water will find its way into your (wooden) boat, due to rain, waves, or leaks. I can hear you saying: But that's what bilge pumps are for! But, my friend, it's a bit more complicated than that.

Way down, deep in your boat's bilge, there is a place where several parts of the boat come together: the keel, the frames, and the hull (specifically the garboard strakes). For strength, the frames usually go all the way across the keel, and sometimes, frames on opposite sides of the keel overlap each other.

But this presents a problem: The keel ends of each set of ribs serves as a wall, dividing the bilge into several compartments. Without any modification, each compartment would independently collect water. Your pump could remove all the water over the tops of the frames and keep the boat from sinking, but it's a bad idea to let water sit in the bilge, because that is asking for your keel and garboards to rot away.

Sometimes the geometry of the boat's construction creates a small gap near the keel between the bottom of each frame and the hull planks. But this is not always the case, and such gaps are frequently too small to be of any use.

The solution to the problem is to drill small holes across the bottom of each frame, right next to the keel (or keelson, if your boat has one). It will weaken the ribs a little, but will also allow water to pass between each bilge compartment. If you place your pump in the compartment at the deepest part of the boat, it will be possible to pump all of the water out.

\___                            ___/
    `--------------------------'      FRAME
`-.                     |        .-' 
`-.`-.________o_.--._o__|_____.-'.-'  HULL
   `------------|  |------------'
                |  |
                |  | KEEL

Limber holes are not advisable in a very small boat with very narrow frames, but since the bilge pump for such a boat is usually a cut-down bleach bottle, and there is usually access to all bilge compartments, this isn't a problem. Fiberglass boats and small metal boats are likely to have limber holes built into the boat's pseudo-frames. And large metal ships will not have limber holes, since they will be built with bulkheads separating watertight compartments (each with its own pumps), to prevent sinking in case the hull is penetrated.