If you use 800 x 600 and it's Ok, why worry? But in an attempt to put you at ease, your monitor may not like the lower resolution which comes from your video card. While your video card may offer more than one resolution (most do), the BEST one to select is the one that is the NATIVE RESOLUTION for your monitor. You'll have to check your monitor's specifications to determine that.
You can try various other resolution settings, but know that the NATIVE resolution is the one you can expect the best images from. Also, resolutions greater than your monitor's NATIVE resolution, will make the screen images larger and larger and they will not fit entirely on the screen.
As I said before, if 800 x 600 is what you use, why worry? And, find out what the NATIVE RESOLUTION is on your monitor and use that (unless it's 640 x 480). Your monitor just doesn't like that lower resolution.
From your description of the problem it would seem that you have an LCD monitor or a fairly large (>14") CRT.
If you have an LCD monitor, know that LCDs have what is called a native resolution. The native resolution defines what resolution the monitor should be set to for optimum image quality. Setting the display to anything else will cause the image to be blurry or improperly rendered. If you have an LCD, find out its native resolution and set your Windows desktop and all your games to run at that resolution.
If you have a CRT, know that the 640x480 resolution is considered outdated and is rarely used on desktop or in other applications. A resolution of 800x600 is considered to be a bare minimum resolution and 1024x800 is considered to be the current standard.
I don't know how much you know about graphics, monitors, and resolutions, so I will give you a little bit of information about what the resolution is. The resolution defines how many pixels will be used to produce an image. More pixels per image generally mean a clearer image with a smoother appearance. Thus, running your display at a resolution of 800x600 or higher will produce better images.
With all of that aside, is there a reason why you want to run games at 640x480?
What type of display and computer do you have?