Stock Intake Manifold

Those holes are called "EGR floor holes" (Exhaust Gas Recirculation) The threaded side is supposed to have a cylinder with holes screwed into it. The otherside was left as you see it.

You can just use a plug on the threaded side. Install the head of the screw flush with the floor.
In the other, non threaded side, it is possible to thread it and and plug it like the threaded side.

These holes are for emmission purposes. The idea of tapping the exhaust gas and reroute the gas back into the cylinders to be reburned in order to reduce emmisions.