I agree it is a problem to get applications working that require a lot of non-core-distribution modules. But I do not think packing everything into the Perl distribution is a good idea. I am also not sure anymore if installing application-specific modules into the standard site_perl directories is always good, either. If you have many applications running on the same system, you sometimes want incompatible versions of the same CPAN module, for example.

I think large Perl applications should include all their dependencies in their own library path, and small applications should get their modules from a user_perl path. In both cases, you do not need superuser rights to manage these installations, which is especially good for shared hosting. Both is already possible, even with the CPAN tool, but it could maybe get easier. For example, when a non-root user does CPAN install it could install into a user_perl directory that would also be automatically recognized by the Perl runtime.

Let me put here my short list.

That list would be very different for everyone. If you include Class:DBI, CGI::Application, Kwiki (very application specific stuff) it will make it difficult to argue where to draw the line.