Instead of hard-coding these, you should add (or reuse) methods on PhabricatorApplication so each application, so the code looks something like this:

foreach ($all_applications as $app) {
  if ($app->shouldThisThingGoOnTheDefaultHomeMenu()) {
    $items[] = new item
  }
}

Then third-party applications will be able to install themselves, etc. I think isPinnedByDefault() is currently the method for this.

You can generate builtin keys like "app.".$app->getPHID() or similar. They just need to be unique; they don't need to be constants.