<action method="addJs"><!-- this will be shown second -->
    <script>prototype/javascript1.js</script>
    <params><![CDATA[name="js002_second"]]></params>
</action>
<action method="addJs"><!-- this will be shown first -->
    <script>prototype/javascript2.js</script>
    <params><![CDATA[name="js001_first"]]></params>
</action>

<reference name="head">
    <block type="core/template" name="fancy" as="fancy" template="fancybox/fancybox.phtml" />
</reference>

<script type="text/javascript" src="<?php echo Mage::getBaseUrl('js').'/fancybox.js'?>"></script>

app/etc/modules/Company_ReorderAssets.xml

<?xml version="1.0"?>

 <config>

     <modules>

         <Company_ReorderAssets>

             <active>true</active>

             <codePool>local</codePool>

         </Company_ReorderAssets>

     </modules>

 </config>

<?xml version="1.0"?>

 <config>

     <modules>

         <Company_ReorderAssets>

             <version>1.0.0</version>

         </Company_ReorderAssets>

     </modules>

     <global>

         <blocks>

             <class>Company_ReorderAssets_Block</class>

             <page>

                 <rewrite>

                     <html_head>Company_ReorderAssets_Block_Page_Html_Head</html_head>

                 </rewrite>

             </page>

         </blocks>

     </global>

 </config>

<?php



 class Company_ReorderAssets_Block_Page_Html_Head extends Mage_Page_Block_Html_Head {



    public function addItemFirst($type, $name, $params = null, $if = null, $cond = null) {



        if ($type === 'skin_css' && empty($params)) {

            $params = 'media="all"';

        }



        $firstElement = array();

        $firstElement[$type . '/' . $name] = array(

            'type' => $type,

            'name' => $name,

            'params' => $params,

            'if' => $if,

            'cond' => $cond,

        );



        $this->_data['items'] = array_merge($firstElement, $this->_data['items']);



        return $this;



    }



    public function addItemAfter($after, $type, $name, $params = null, $if = null, $cond = null) {



        if ($type === 'skin_css' && empty($params)) {

            $params = 'media="all"';

        }



        $firstElement = array();

        $firstElement[$type . '/' . $name] = array(

            'type' => $type,

            'name' => $name,

            'params' => $params,

            'if' => $if,

            'cond' => $cond,

        );



        if (array_key_exists($after, $this->_data['items'])){



            $pos = 1;

            foreach ($this->_data['items'] as $key => $options){

                if ($key == $after) :

                    break;

                endif;

                $pos +=1;

            }



            array_splice($this->_data['items'], $pos, 0, $firstElement);



        }



        return $this;



    }
 }

<?xml version="1.0"?>

 <layout version="0.1.0">

    <default>

         <reference name="head">

            <action method="addItemFirst"><type>skin_js</type><script>js/jquery.js</script></action>

            <action method="addItemAfter">

                <after>skin_js/js/jquery.js</after>

                <type>skin_js</type>

                <script>custom_folder/javascript.js</script>

            </action>

            <action method="addItemAfter">

                <after>skin_js/js/jquery.js</after>

                <type>skin_js</type>

                <script>custom_folder/another_javascript.js</script>

            </action>

         </reference>

    </default>

 </layout>