I have additionally compiled the SDL flavour of fuse, in order to get full screen mode. I am not actually surprised that it completely fills the screen, but it does result in things looking wider than they ought to on my 16:10 ratio screen.
Whereas that might be desirable sometimes, I am wondering if it might be possible to have a "full height, 4:3" mode available by some means. Is this likely to be possible, or is it perhaps already easy?
For testing purposes, you could try the patch http://sourceforge.net/tracker/?func=detail&aid=3152071&group_id=91293&atid=596650. However, this patch enables fullscreen mode as "maximum scaler 4:3" instead of "full height 4:3", and it's done for GTK flavor.
This is because the OS/graphics driver tells SDL Fuse that it supports a fullscreen mode like 800x600 which Fuse innocently tries to select thinking it will be a traditional 4:3 image and your OS/graphics driver tries to "help" by stretching to occupy all your 16:10 screen. There can be an option about to not do that in your graphics/OS setup sometimes, but the SDL graphics APIs don't tell you the aspect ratio of the resulting full screen.
I can confirm that I have found a setting on at least one of my systems that centres rather than stretches.