When I change the screen resolution in game, in windowed mode, all it does is change the shape of the window. So I stretch it out to max and it's still the same resolution 640 x 860. Is there a way to change the resolution so that in windowed mode, it looks pretty close to full screen at larger resolutions?
Yes - Under display options you can select the windowed resolution. When you grab the corner and drag you are scaling the 640x480 base which gives you nice fat pixels.
For me in windowed mode I can usually drag the EQ screen to the top of the physical screen and it autosizes to the monitors full resolution (or whatever resolution its currently running at).