If the floor is really uneven, putting click-lock laminate (Pergo) directly on it will cause problems. The stuff really doesn't like to bend. If it's a slight waviness that might be OK.

As for home theater wiring, install PVC conduit (either the stiff gray stuff or that blue flex stuff Carlon makes). The way technology changes, you'll want to be able to pull new cables through without tearing up the walls or running cables on the surface. Use the largest conduit you can successfully conceal in the walls.