The biggest part I have been using is the keyboard becoming a track pad. I like the quick cursor feature for editing, its faster than trying to land in just the right spot when dragging over text. I have tried to incorporate the feature with other apps but really have not found it to be way faster yet. If iOS 9 had not added a link in the top left to go back to the previous application I would peek more often but with an easy way to return to where I was its not been a big deal to go ahead and just follow a link with a tap.
My three most frequent uses so far are on the keyboard to freely move the cursor around for an edit, left side of screen in lieu of a home button double tap and a peek into mail maybe followed by a swipe to trash.
I use it quite a bit to open the multitasking cards. Occasionally I use it for shortcuts to apps, but there are far too few that have added that functionality for me to be able to remember to use it regularly. I have to consciously think about using it that way, where using 3D Touch to open the app switcher is pretty much ingrained for me at this point. I don't use the peek and pop too much yet, to be honest.