Installing phpmyadmin puts /javascript in the Apache global namespace in Squeeze because javascript-common is a dependency of libjs-mootools and lib-mootools is a dependency of phpmyadmin, and javascript-common does this.

However /usr/share/phpmyadmin maps (some!) mootools files into its namespace by using symlinks rather than relying on /javascript, so commenting out the mapping doesn't appear to break phpmyadmin and fixes the broken websites that used "/javascript" to store their javascript.

I can understand the desire for a common namespace, but for the case of hosting multiple website the namespace choice is naff, and it potentially broadens the impact of errors in the Javascript (since it affects all sites hosted on Debian rather than those using the javascript in question). The use of symlinks and/or names under a particular prefix /phpmyadmin/_name would seem to resolve this and allow coexistent of multiple versions (which would seem likely to be relevant in future).