Avoiding dynamic RegEx creation in JavaScript
You can store the regex as part of the smily metadata.

var replaceTextSmilies = function() {
    var smiliesShortcut = {};
    smiliesShortcut[':)'] = {
        img : 'smile.png'
    };
    /* adding much more */

    var smiliesWordy = {};
    smiliesWordy[':angry'] = {
        img : 'angry.png'
    };
    /* adding much more */

    addRegex(smiliesShortcut);
    addRegex(smiliesWordy);

    function escapeRegExp(str) {
        return str.replace(/([.?*+^$[\]\\(){}|-])/g, "\\$1");
    }

    function addRegex(smilies) {
        Object.keys(smilies).forEach(function(smily) {
            smilies[smily].regex = new RegExp('(' + escapeRegExp(smily) + ')(?=(?:(?:[^`]*`){2})*[^`]*$)', 'g');
        });
    }

    function replace(text, smilies) {
        Object.keys(smilies).forEach(function(entry) {
            var image = '&lt;img src="img/smilies/' + smilies[entry].img + '"/&gt;';

            if (text.indexOf(entry) !== -1) {
                text = text.replace(smilies[entry].regex, image);
            }
        });
        return text;
    }

    return function(text) {
        text = replace(text, smiliesWordy);
        text = replace(text, smiliesShortcut);
        return text;
    };
}();


Demo: Fiddle

Note: You can make it even better if you can manually create the regex and assign them instead of using addRegex() like

    smiliesShortcut[':)'] = {
        img : 'smile.png',
        regex: /&lt;the regex&gt;/
    };