Google Voice was gmail-only for a long time.

Google Plus was as well.

Currently, I am waiting for Google Now's gmail integration to get on apps already: http://support.google.com/nexus/bin/answer.py?hl=en&answ...

Those are just services that have/are affected/ing me; I'm certain there are plenty of other examples.

I can't speak for the parent, but an issue in this vein that most recently affected me is the months it took google to allow GApps customers to create a google+ account with their apps login.

Gmail for Apps still can't auto-add people to your chat list, even though the option is there.