5.25" fits optical drives, fan controllers, etc. 3.50" fits hard drives, but hard drives can be fit in 5.25" bays with an adapter. Also, 3.50" bays are all internal.
So if I was looking at a case with 4 5.25" bays and I only needed 1 optical drive it'd be pretty useless? Do the bays show on the outside if there is no door for the case?