First, is there anyway to improve the graphics on Stone keep without making the game run in a small window. I'm not interested in a user made patch, just maybe something to change in the config file.
First, try the different graphics options in the "Graphic Mode Setup" utility provided by GOG. It should be on the start menu in the same location as Stonekeep.
Second, you can make the window bigger pretty easily (although this does not affect the quality of the graphics, it just scales them up). To do this, find the configuration file in the game directory (dosbox_stonekeep.conf or something similar), open it in notepad or another text editor, and look for the line that says "windowresolution=original". Change that to any resolution you want, for example "windowresolution=1024x768". The game will then scale up to that size, although it will still be running at the same resolution, just stretched.
You can also play with the scaler settings in the configuration file, but I don't have a lot of experience with those. More info here: http://www.dosbox.com/wiki/Dosbox.conf#.5Brender.5D