I have exactly this problem, slightly bigger - currently 46 vhosts running between them 6 different versions of an application - and I've avoided mod_perl for now precisely because of the problem of multiple library versions. I understand that v2 mod_perl does/will fix this problem.

Under v1 it might be possible to work around this problem if each module user knows (or can reach an object that knows) what version of each module it needs. It'd be a bit of a pain, but I can imagine replace each use My::Module; with $application->load_module('My::Module'), and (roughly):

sub Application::load_module {
  my($self, $class) = @_;
  return 1 if do {
    no strict 'refs';
    # may need string eq here
    ${"${class}::VERSION"} == $self->required_version($class);
  };
  (my $path = "$class.pm") =~ s{::}{/}g;
  delete $INC{$path};
  require $path;
}
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It may also be possible to roll up something similar at a lower conceptual cost using Ingy's only.

Hugo