I run most apps as close to full screen as possible both on my OS X box at work and on my Linux box at home on separate spaces / virtual desktops. On both the only thing visible apart from the maximized app window is a menu bar / systray. For apps I can do it with easily, I've removed the window title bar (you can easily do this with a theme on Linux and/or by twiddling with "full screen" settings). I've got one virtual desktop set aside for file management etc. similar to having a Workbench screen.
Effectively I'm manually hacking together something that halfway sort-of tries to act like AmigaOS