A good example is let's say I'm making a pong game. I have a PNG image for the ball and another PNG image for the paddles. Now which would be better, loading the PNG images with a PNG loader, or loading them in a separate program, serializing it, and de-serializing it in the game itself for use?

The reason why this may be good to know is because it seems like game companies (or anyone in the long run) build all of their resources into some sort of file. For example, in the game Fallout: New Vegas the DLCs are loaded as a .ESM file, which includes everything it needs, all the game does is find it, serialize it, and it has the resources. Games like Penumbra: Black Plague take a different approch and add a folder which contains all the textures, sounds, scrips, ect that it needs, but not serialized (it does this with the game itself, and the DLC).

Which is the better approch and why?