Drive bays? Those are places to put drives...Hard drives, floppy drives, or CD/DVD drives. The big ones that hold CD drives are 5.25", the ones that hold standard hard drives are 3.5" and usually internal, and the ones that hold floppy drives are 2.5". Typically, random gadgets like card readers and fan controllers will go in a 2.5" bay, since most people don't use floppy drives anymore. You also see those in 5.25", but it's not quite as common.
Laptop hard drives and solid state drives are also 2.5", but they're quite a bit thiner than a 2.5" bay.