I also think it is reasonable to continue offering a feature like dependency_links on an opt-in basis for controlled environments (I see it as analagous to the direct references feature in PEP 440).
with pip already, the idea** is that you can enforce a concrete location for a dependency that will override the default pypi location. e.g. I can do pip install http://myserver/peppercorn-0.3.tar.gz#egg=peppercorn deform (where deform requires peppercorn) and my peppercorn will be installed the point being, I don't think we need setup.py dependency links to be able enforce concrete url fulfillment. ** I say "idea", because I know there are bugs related to archive urls and egg fragments and overriding other dependencies, but the point still stands.