You do not tell, but the example below is for the 4.x version of XFree.
Edit your /etc/X11/XF86Config
Find the Section "Screen" section.
If there is a DefaultDepth 16 entry below it (16 may be different), remember the number (16 in this case)
Look for the SubSection "Display" that has the Depth 16 (16 being the important part)
The line below that should look something like this:
Modes "800x600" "640x480"
You might have guessed that the 800x600 and 640x480 are resolutions. In this case there are 2 resolution available, X will always use the first one (800x600 in this case) if not changed/overwritten.
Removing the 800x600 part, or placing it at the end of the line will make the 640x480 default.
You do need to restart X to make this change known to X and its environment.
Hope this helps.