Marval - 2:03 pm on Feb 1, 2006 (gmt 0)

While I agree that the htaccess method is good and personal experience shows it works well with Google, I would also recommend checking (assuming you are using an Apache/Nix installation) for the server config Servername statement and verify it is set to www.domain.com and not domain.com - If it is the latter, any time you have a directory link, i.e. href="/newdir"
apache sees that it is a directory, issues a 301 redirect with the ServerName which would be a backdoor for Googlebot to find dupes (this is an issue I tried to bring up to googleguy some time ago when the canonical issue came about with their issue of the new bot software they use back in 2004 but I believe it got passed on to the engineers and then kinda got ignored)