Is Gaff hunting Deckard and Rachel or what?
I doubt it. The ending makes it pretty clear (well as clear as anything is really made clear in the movie) that he was there waiting to take them out and changed his mind.
Still, Scott shouldn't have made Deckard a replicant. I mean, the movie itself is completely different from the source material anyway, but Decker is meant to be human and is confirmed as such in the book. Besides, the original release basically leaves the question completely unresolved, and the directors cut handles the answer rather hamfistedly.
I always thought that Gaff had come by when Deckard wasn't there, and Deckard just didn't see the origami unicorn in his initial haste to get to the apartment.
Gaff did come by when Deckard wasn't there. He was originally planning on ambushing them, and changed his mind. He left the origami as a literal token gesture of indicating that he could have killed Deckard anytime he wanted to, and could have now as well. The implication is that Deckard hasn't gone crazy, so Gaff really isn't going to bother.