To start a game in windowed mode, create a shortcut to RPG_RT.exe and add the following parameters:
NormalPlay ShowTitle Window
I also wrote a tool which stretches the game to fullscreen without changing the resolution, it also allows you to apply a filter (Scale2x or hq2x) for better graphics.
http://cherrytree.at/downloads/afm.rarThis is a little tool which lets you play RPG Maker 2000/2003 games in fullscreen - without changing the resolution. This is a workaround for people who have problems with their screen or their graphics driver. AnotherFullscreenMode needs at least a 1 GHz CPU to run without lagging.
First, start your game (in windowed mode). Then start AnotherFullscreenMode. By pressing F6 you can switch between fullscreen and windowed mode, F7 shows or hides the FPS.
Using F8, you can set the filter: none -> Scale2x -> hq2x
Example screen with hq2x (in windowed mode):