I see a few strange things, but it could be because I don't completely understand what kind of objects these are supposed to be. Are they just an OOP wrapper API to these config files, or do they have other purposes? It seems like you're trying to have accessors defined on a per-object basis (you (re)generate the accessors every time the new method is called). But you create these accessors on a per-class basis, and all of your objects are of the same class. Do you only ever instantiate one of these OurApp objects per execution of your app?

The way I understand it, I could write the following:

use OurApp;

my $obj1 = OurApp->new(conf_file => 'conf1');
my $obj2 = OurApp->new(conf_file => 'conf2');

# can use both foo and bar accessors on BOTH objects

print $obj1->foo, $obj1->bar;
print $obj2->foo, $obj2->bar;

__END__
conf1 contains:
  foo=1
conf2 contains:
  bar=1
[download]

Wouldn't you want $obj1->bar and $obj2->foo to give an error like Can't locate object method "bar" via package "OurApp"? It won't happen if the OurApp namespace has been given both methods. Of course, if you don't plan on having multiple OurApp objects around this isn't a problem.

blokhead