Now that I think about it, maybe I have the components of my name spacing all backwards! This all might make a lot more sense if instead of Whatever::Link::Query and Whatever::Object::Query I had Whatever::Query::Link and Whatever::Query::Object. In fact, I think that's perfect... Each of those could probably benefit (though I'm not yet sure how) from a common Whatever::Query base class. Furthermore, I could then use the Object subdirectory strictly for subclasses of Whatever::Object. This fixes all of my quandaries.

I like this the best. Feels good to me :)

Am I crazy for even considering this?

Of course you are, but that shouldnt surprise you, no doubt you have been crazy all your life, otherwise you wouldnt be a perl programmer :)

Is there a more elegant way of doing what I want to do?.

Well, I have had to solve this problem in particular myself, and I always kind of liked the way I did it. I has worked for me quite successfully for a little while now. Here is an example using your namespace:

package Whatever::Object::DBDAgnostic;

use strict;
use warnings;

sub import {
    # only set this once
    return if scalar @Whatever::Object::DBDAgnostic::ISA;
    my (undef, $base_class) = @_;
    die "You must define a DBD-type" unless $base_class;
    push @Whatever::Object::DBDAgnostic::ISA => $base_class;
}    
    
1;
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Then all your users need to do is:

package Foo;

use strict;
use base qw/Whatever::Object::DBDAgnostic/;

# decorator methods go here

1;
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Then in order to set what DBD subclass is to be used you, all your user needs to do this:

use Whatever::Object::DBDAgnostic qw(Whatever::Object::MySQL);
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Before any other code that uses Whatever::Object::DBDAgnostic is loaded, and your Whatever::Object::DBDAgnostic::ISA should be good. Sure its an extra level of inheritence, but it pays for itself in flexibility. Also keep in mind that perl's method caching will pretty much make a performance cost to null in a long running system like mod_perl.