Chuck D. Bones
Circuit Wizard
In the right circuit, they can impart a smoother tone, fewer high-order harmonics.
And then there's the MOJO factor.
And then there's the MOJO factor.

I've seen clear protoboards for sale, but have yet to buy one. I think they look cool.
...
IMO ... it's a subtle difference, but WHITE is just plain easier on the eyes to see what's what while you're working.