The error “The configuration file now needs a secret passphrase (blowfish_secret).” occurs on Debian 6 Squeeze because computers are shit and everyone sucks balls at writing software properly.
To fix this, you need to manually add a key to the config. This is assuming you already have the config, and that you don’t need to copy/rename the sample config.
Go to this site to get a key: phpMyAdmin Blowfish Secret Generator.
You enter that key into config.inc.php, in your phpmyadmin directory. Debian is usually /etc/phpmyadmin.
Enter it into/add the following line:
$cfg['blowfish_secret'] = 'BLOWFISH PASSWORD HERE';
Obviously, you replace the giant letters, that tell you where you put your key, with the key.
The first link I found, when I searched for this, was most useful: Question Defense.
It’s really sad that some packages are still this broken, after more than four years. I experienced this issue for the first time on an x64 build of Debian 6, though I’ve since been met with it on any version of Debian 6.
Debian 7 Wheezy also has this issue, though the configuration file format has been changed somewhat and now the passphrase goes into its own file in /var/lib/phpmyadmin. At least in Debian 7 it gives you information on what it means and how to use it (somewhat) if you look at the config files.