Off the top of my head: (and posted as they come to mind, not in chronological order)
Which sibling survived Lothering (based on which class you chose)
Whether the surviving sibling died in the Deep Roads, became a templar, a Warden, or was taken to the Circle
Whether you sided with Mages or Templars in the end;
Whether you killed or spared Anders (I think the importance of this choice will revolve around Sebastian Vael, not Anders himself, given Sebastian's threats to Hawke based on your choice here). Obviously depends on whether you played Sebastian's DLC.
Whatever fate you decided for Feynriel, the elven Somniari.
There were other choices, of varying import (and none as important as these, in my opinion), but I think the above are the ones that are most likely to have some degree of impact on Inquisition. Of course, it's late, and I might've missed a few.
Oh! One other thing that does come to mind is whether or not Petrice survives DA2, depending on your choice. If she's alive, I'd not be surprised for there to be a side quest involving her, given her extremist views regarding the Chantry and the measures she's willing to take to spread the faith.