> just found HTTrack and it is a really great problem

Say what?!

> All the links on my site use a javascript function like > this one :

> <script language="JavaScript">
> function ChargerDoc(s, catid)
> {
>         window.parent.gauche.location =
> 'gauche.php?s='+s+'&m=2&p=43&catid='+catid+'&d=&ss=&sss=';
>         window.parent.droite.location =
> 'documents.php?s='+s+'&m=2&p=43&catid='+catid+'&d=&ss=&sss=';
> }
> </script>

> and my links are made like that :
> <a href="#" onClick="ChargerDoc('HGDS0JUD70', '532');" class=txt1>Text</a>

Then why don't you just do the obvious?Use HTTrack with URLs like:

<http://www.chezJulien.com/gauche.php?s=HGDS0JUD70&m=2&p=43&catid=532&d=&ss=&sss>=

and 

<http://www.chezJulien.com/documents.php?s=HGDS0JUD70&m=2&p=43&catid=532&d=&ss=&sss>=