Вот так и настраивай.
Все строчки должны иметь вид
<VirtualHost *:80>
Никаких
<VirtualHost site.ru>
AnrDaemon спасибо большое за помощь! Теперь работает

Конфиги сайтов те же что в первом сообщении, только изменил
<VirtualHost site.ru:8080>
<VirtualHost stat.site.ru:8080>
на <VirtualHost *:8080>
и в /etc/apache2/ports.conf изменил NameVirtualHost *:80 на NameVirtualHost *:8080
root@site:/etc/apache2# apache2ctl -MS
[Tue Sep 21 18:28:20 2010] [warn] module rpaf_module is already loaded, skipping
VirtualHost configuration:
wildcard NameVirtualHosts and _default_ servers:
*:80 sitevds (/etc/apache2/sites-enabled/000-default:1)
*:8080 is a NameVirtualHost
default server site.ru (/etc/apache2/sites-enabled/site.ru:1)
port 8080 namevhost site.ru (/etc/apache2/sites-enabled/site.ru:1)
port 8080 namevhost stat.site.ru (/etc/apache2/sites-enabled/monitoring:1)
Loaded Modules:
core_module (static)
log_config_module (static)
logio_module (static)
mpm_prefork_module (static)
http_module (static)
so_module (static)
alias_module (shared)
auth_basic_module (shared)
auth_digest_module (shared)
authn_file_module (shared)
authz_default_module (shared)
authz_groupfile_module (shared)
authz_host_module (shared)
authz_user_module (shared)
autoindex_module (shared)
cgi_module (shared)
deflate_module (shared)
dir_module (shared)
env_module (shared)
mime_module (shared)
negotiation_module (shared)
php5_module (shared)
reqtimeout_module (shared)
rewrite_module (shared)
rpaf_module (shared)
setenvif_module (shared)
status_module (shared)
Syntax OK
root@site:/etc/apache2# /etc/init.d/apache2 restart
* Restarting web server apache2 [Tue Sep 21 18:28:36 2010] [warn] module rpaf_module is already loaded, skipping
... waiting [Tue Sep 21 18:28:37 2010] [warn] module rpaf_module is already loaded, skipping
[ OK ]
PS порт 8080 потому что у меня на 80 стоит nginx