There might be an issue with the .htaccess file
You can do some tests by uploading files such as hello.txt containing just hello and create some directories with this file in them for basic testing where you surf to the URL.
But error 404 means that the URL can't be resolved, so like other people mentioned, it is likely to be a .htaccess error where it is redirecting to a non-existent place.
I had this happen 'Page Not Found' happen again while trying to log onto another site running wordpress 2.9.1. The .htaccess file is fine. I checked by logging on via ftp.
Upgrading to wordpress 3.04. But kind of a pain.
The login page is out of wack. Perhaps a couple of wordpress files were damaged in a hacking attempt.
The problems sites are using wordpress 2.9.1 and upgrading to wordpress 3.04 resolves the problem.
I did have that problem with my first attempt to password protect the WordPress admin area. The standard .htaccess/.htpasswd method for password protection does not work with WordPress, but there is a workaround. It is possible that they fixed that problem with 3.0.4.
Is your admin area password protected with .htaccess?
Is this issue where the standard login worked for quite a while and all of a sudden ceased working? That would be a strange problem.
"Democracy is two wolves and a lamb voting on what to have for lunch. Liberty is a well-armed lamb contesting the vote." -- Benjamin Franklin
Upgrading to Wordpress 3.04 via ftp resolves the problem.