We have an internal system for tracking our internal applications. We use Applications in CA PPM to log those internal apps (no auto feed yet) and use Project Dependencies to set up the dependency. A custom report was created so that we could report on those dependencies.
This also allows our PM to check to see if any other project has a dependency on the same internal app.
When an app is not listed, they send the relevant information to our support team and the app is added, The PM is then notified and they can create the dependency. A very simple process and it works. The turn around time is normally about an hour or so.