There is a resolution changing script by Glitchfinder, which changes the window size without distorting anything in the window, effectively changing the resolution.
After using it, you have to reposition all windows, but that's done quickly.
so you could go from 640x480 to 1920x1080 (if you wanted, it would lag like hell)
Problem is, is that when you Alt-Enter, it cuts the screen down to 640x480 again, and all of your stuff doesn't auto-resize (obviously) and everything's out the screen. If you un-fullscreen, its still stays at 640x480, with all of your stuff out the window (aha, 'out the window')
You have to restart the game to reset it. That's the problem.