You could use something like LDAP, which should allow both NT and *NIX platforms to authenticate against it. You can set it up to do anything from application level authentication (what you want), to web basic auth, and even workstation or network logins. It allows you to have one single authentication system, rather than multiple "databases" to maintain.

Perl has quite a rich interface to this directory service. Do a search on CPAN for the word LDAP, or check out Net::LDAP, and you'll see what I mean.