I think to be more correct, you should be talking about designing a shell and a file manager, rather than an entire OS. In Windows you're limited on both counts, but it's possible to replace your shell with a different one that looks and acts completely different (LiteStep and Aston Shell are two examples). Ontrack used to make a replacement file manager for Explorer, but I don't believe it's available any longer. (Isn't Microsoft retarded? The shell, the file manager, and the web browser are all entirely different things, but are confusingly called "Explorer"..)
In Linux, there is no one particular "look", and there is a hell of a lot more customizability than there is in Windows.