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In my header.php, where I want qTranslate language chooser to live, I put this in:

<?php echo qtrans_SelectCode('code');?>

Then, I added this code to functions.php. It's a little redundant in that it repeats the built-in qTranslate options (image, text, dropdown) which I am not using on my page - but I wanted to retain the code since my filter is overwriting the qtrans_generateLanguageSelectCode function. (If anyone can figure out how to just ADD a style in and not overwrite the whole function, that would be awesome!)

The style that I use is called 'code' (you'll see it near the bottom) and just outputs the language code - ie: FR and EN in my case. You could write whatever output you want by creating a new style:

if( function_exists( 'qtrans_getLanguage' ) )
{
// qTranslate Language Select Code filter

    add_filter( 'qtrans_generateLanguageSelectCode', 'qtrans_SelectCode' );

    function qtrans_SelectCode( $style = '', $id = '' ) {
        global $q_config;
        if( $style == '' )
            $style = 'text';
        if( is_bool( $style ) && $style )
            $style = 'image';
        if( is_404() )
            $url = get_option( 'home' );
        else
            $url = '';
        if( $id == '' )
            $id = 'qtranslate';
        $id .= '-chooser';
        switch( $style ) {
            case 'image':
            case 'text':
            case 'dropdown':
                echo '<ul class="qtrans_language_chooser" id="' . $id . '">';
                foreach( qtrans_getSortedLanguages() as $language ) {
                    $classes = array( 'lang-' . $language );
                    if( $language == $q_config['language'] )
                        $classes[] = 'active';
                    echo '<li class="' . implode( ' ', $classes ) . '"><a href="' . qtrans_convertURL( $url, $language ) . '"';
                    // set hreflang
                    echo ' hreflang="' . $language . '" title="' . $q_config['language_name'][$language] . '"';
                    if( $style == 'image' )
                        echo ' class="qtrans_flag qtrans_flag_' . $language . '"';
                    echo '><span';
                    if( $style == 'image' )
                        echo ' style="display:none"';
                    echo '>' . $q_config['language_name'][$language] . '</span></a></li>';
                }
                echo "</ul><div class=\"qtrans_widget_end\"></div>";
                if( $style == 'dropdown' ) {
                    echo "<script type=\"text/javascript\">\n// <![CDATA[\r\n";
                    echo "var lc = document.getElementById('" . $id . "');\n";
                    echo "var s = document.createElement('select');\n";
                    echo "s.id = 'qtrans_select_" . $id . "';\n";
                    echo "lc.parentNode.insertBefore(s,lc);";
                    // create dropdown fields for each language
                    foreach( qtrans_getSortedLanguages() as $language ) {
                        echo qtrans_insertDropDownElement( $language, qtrans_convertURL( $url, $language ), $id );
                    }
                    // hide html language chooser text
                    echo "s.onchange = function() { document.location.href = this.value;}\n";
                    echo "lc.style.display='none';\n";
                    echo "// ]]>\n</script>\n";
                }
                break;
            case 'both':
                echo '<ul class="qtrans_language_chooser" id="' . $id . '">';
                foreach( qtrans_getSortedLanguages() as $language ) {
                    echo '<li';
                    if( $language == $q_config['language'] )
                        echo ' class="active"';
                    echo '><a href="' . qtrans_convertURL( $url, $language ) . '"';
                    echo ' class="qtrans_flag_' . $language . ' qtrans_flag_and_text" title="' . $q_config['language_name'][$language] . '"';
                    echo '><span>' . $q_config['language_name'][$language] . '</span></a></li>';
                }
                echo "</ul><div class=\"qtrans_widget_end\"></div>";
                break;

            case 'code':
                $count = 0;
                foreach( qtrans_getSortedLanguages() as $language ) {
                    if( $count > 0 )
                        print '  ';
                    $count++;
                    if( $language == $q_config['language'] ) {
                        print '<span class="qtrans_language_chooser active" title="' . $q_config['language_name'][$language] . '">';
                        print $language;
                        print '</span>';
                    }
                    else {
                        print '<a href="' . qtrans_convertURL( $url, $language ) . '" class="qtrans_language_chooser"';
                        print ' hreflang="' . $language . '" title="' . $q_config['language_name'][$language] . '">';
                        print $language;
                        print '</a>';
                    }
                }
                break;
        }
    }      
}

It is important to enclose the functions in:

if(function_exists('qtrans_getLanguage'))

in case the qTranslate plugin breaks or you deactivate it, otherwise your functions.php will not work properly and you won't be able to get at your site!

Sorry I took a little while to get back, I am not a web developer by profession so I haven't touched this stuff in a few months. I'm completely self-taught, which is why my terminology may be a little unclear. But I hope this helps!