Looks like there was a quite silent change in the format of apache’s config files from ubunutu hardy to intrepid (maybe related to the move from debian to its etch release).

Ports.conf now has a statement

NameVirtualHost *:80

Which means all the vhost files (as in /etc/apache2/sites-enabled) need a directive :

<VirtualHost *:80>

Important part is the :80 statement. If missing, this leads to strange

[warn] default VirtualHost overlap on port 80, the first has precedence

error messages.