I count each volume as one complete book. For instance, I am also reading a Poe collection, but when I catalog it in LibraryThing and in my Book Collector software, it will be one book. I can mention all the stories separately when I'm discussing Poe with someone, but I will only list the collection as one book, with one ISBN. I always list The Lord of the Rings as one complete book, which it is. It was never meant to be a trilogy, even though many people own three separate books. I bought a one-volume edition specifically for the fact that it's the way Tolkien wanted it. I'm not as sure about the Narnia series, because it seems more like an intended series, with separate books. If I had them, I would probably list them separately, unless I had bought them in a one-volume edition.
In the end, though, you should do what makes you comfortable! These things tend to weigh on my mind somewhat (I'm a compulsive cataloger), so I understand your troubles. I hope I've helped, at least a little bit!