for websites using fancy encodings (ie different of your default server
encoding), you will need to configure your server to set the default encoding
aproprialy for each site. 

For example if the site "foo/" uses iso 8859 while your server is configured
for utf8 by default you will need to modify your etc/apache2/apache2.conf like
this

<Directory /var/www/websites/foo/*>
   AddDefaultCharset iso-8859-1
</Directory>

since httrack seems to be unable to convert on-demand the encoding of a whole
site.