A bookmarklet for applying a custom style to Kindle Cloud Reader (applies a sepia theme with a higher contrast similar to iBooks on iPad; increases the size of fonts that are too small). Use a tool like http://ted.mielczarek.org/code/mozilla/bookmarklet.html to convert it to a one-liner and use it as a bookmarklet.

kindle-cloud-reader-custom-sepia.js

function applyCustomStyle() {
    var config = {
        backgroundColor: "rgb(246, 239, 220)",
        foregroundColor: "rgb(64, 41, 25)",
        highlightColor: "rgb(255, 245, 173)",
        codeFontSize: "12px"
    };

    var masterFrameContents = $("#KindleReaderIFrame").contents();
    var pageFrameContents = masterFrameContents.find("iframe").contents();

    var removeFooter = function() {
        masterFrameContents.find("#kindleReader_immersiveFooter").remove();
    };

    var enlargeSmallCodeFonts = function() {
        pageFrameContents.find("code span, tt span")
            .each(function() {
                this.style.setProperty("font-size", config.codeFontSize, "important");
            });
    };    
 
    var themeElement = function(elem) {
        elem.style.setProperty("background-color", config.backgroundColor, "important");
        elem.style.setProperty("color", config.foregroundColor, "important");
    };

    var themeHighlight = function(elem) {
        elem.style.setProperty("background-color", config.highlightColor, "important");
    };
 
    var applyCustomColorScheme = function() {
        pageFrameContents.find(".amzUserPref")
            .each(function() { themeElement(this) });
        
        masterFrameContents.find("#kindleReader_book_container, #kindleReader_center, #kindleReader_content div, .kindleReader_pageTurnArea")
            .each(function() { themeElement(this) });

        masterFrameContents.find("iframe").each(function() {
            $(this).contents().find(".amazon-highlight").each(function() {
                themeHighlight(this);
            });
        });
    };

    removeFooter();
    enlargeSmallCodeFonts();
    applyCustomColorScheme();
};

applyCustomStyle();

Night mode:

    var config = {
        backgroundColor: "rgb(57, 59, 61)",
        foregroundColor: "rgb(203, 207, 208)",
        highlightColor: "rgb(53, 91, 135)",
        codeFontSize: "12px"
    };