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!