At least this works when you want to have 1280x1024 resolution in the game (very nice if you have 17" TFT display). I'm not sure if 640x480 is even possible, but try this.
If you have Conquests, open the conquests.ini with notepad and add there a line which says:
KeepRes=1
That will make Civ3 Conquests use your desktop resolution. If you don't have Conquests, you must open civilization.ini (or something like that, you'll find it).