ng-annotate works just fine with regular angular controllers/filters/providers/services/etc. definitions, but I would not trust it for special injections found in such stuff such as $state definitions with resolves and maybe $get with the factory returned by a provider.
it can certainly not support everything, partly because of limitations imposed by static analysis, buy you may be surprised with what it can handle.
Also: For situations where you don't know whether ng-annotate will detect a form or not (assuming you already use ng-annotate for your project), you can use explicitly use /* @ngInject */ or ngInject() to avoid stuttering the array yourself.
