Don’t forget Spirited Away which automatically hides background applications after a time period you specify. I use it with MenuShade to keep my desktop nice and tidy.
MegaZoomer is great, but you don’t need it for Scrivener - just hit Cmd-Ctrl-= (that’s the Command, Control and equals keys simultaneously) to zoom the window to fit your screen, regardless of whether it needs to be made smaller or larger.
I use another option to keep my working surface (i.e., not the desktop, which I never have used for anything) clean:
Using DragThing–as indispensable as Scrivener!–tick off ‘Hide other applications when switching’ in the General Preferences tab. As this can be easily toggled with a customizable hotkey combination, you can have the best of all worlds. I use Screenshot Helper to hide the desktop.
\Of course, using DragThing in this way does rule out floating windows, etc., but it is seamless otherwise.