This should do it. Put a copy of jquery-1.4.2.min.js in the same directory (jQuery is a Javascript library for keeping browser compatibility bugs at bay).

<script type="text/javascript" src="jquery-1.4.2.min.js"></script>
<script>
function setColorScheme(colorScheme)
{
setCookie("colorScheme", colorScheme, 30);
if(colorScheme=="whiteOnBlack")
{
$("body").css({
"background-color": "black",
"color": "white"
});
}
else if(colorScheme=="blackOnWhite")
{
$("body").css({
"background-color": "white",
"color": "black"
});
}
}
$(document).ready(function()
{
var cookie = getCookie("colorScheme");
if(cookie)
setColorScheme(cookie);
});
function setCookie(c_name,value,expiredays)
{
var exdate=new Date();
exdate.setDate(exdate.getDate()+expiredays);
document.cookie=c_name+ "=" +escape(value)+
((expiredays==null) ? "" : ";expires="+exdate.toUTCString());
}
function getCookie(c_name)
{
if (document.cookie.length>0)
{
c_start=document.cookie.indexOf(c_name + "=");
if (c_start!=-1)
{
c_start=c_start + c_name.length+1;
c_end=document.cookie.indexOf(";",c_start);
if (c_end==-1) c_end=document.cookie.length;
return unescape(document.cookie.substring(c_start,c_end));
}
}
return "";
}
</script>
Background color: <a href="javascript:setColorScheme('blackOnWhite')">white</a> | <a href="javascript:setColorScheme('whiteOnBlack')">black</a>

This stores the color scheme in a cookie, so it's preserved when you move between chapters. The setCookie and getCookie functions came from here. Given the example, this should be pretty easy to extend for things like changing text size and margins, if you are so inclined.