My list of "best" correlates perfectly with my list of "favourite":
1: Prisoner of Azkaban - This one was perfect, with wonderful harmony between the safe world of Hogwarts and the dangers of the outside. In no book the "Hogwarts" feeling is stronger, it feels such a tight-knit, warm little community. The books take a mature turn here. And, perhaps most of all, so many of the characters introduced showed potential: Sirius, Lupin, Peter, Buckbeak, Cho, Cedric.
2: Goblet of Fire - Maintains the "Hogwarts" feeling, but a tendency that was to mar later books started here: The trite antagonism of minor characters against Harry. Still, a very good book, bringing along a whole new dimension of complexity with Crouch senior and junior.
3: Deathly Hallows - Might have been rated second, but with Hogwarts being largely absent, this does not hold the same wonder and comfort as #3 and #4. Still, loads and loads of memorable scenes.
4: The Philosopher's Stone - This book introduced the universe with a bang. The Hagrid sequence on the little island - isn't it every child's dream, to discover he/she's someone completely else than initially thought? Of course, there's a very strong "Hogwarts" feeling, but seen in hindsight, the book is far less exciting than those that were to come.
5: The Order of the Phoenix - The "Hogwarts" feeling was rapidly diminishing, but the large character gallery, and the death and its emotional aftermath makes this a book I like rather than dislike. Nevertheless, the anti-Harry antagonism is stronger here, and I was very disappointed to see that Cho Chang was such a shallow character after all. This book is where the problems of HP characterization get visible: Anyone outside of Harry's closest bunch of associates is by default stupid, unsympatethic and potentially evil.
6: Chamber of Secrets - This book just felt generally childish. Dobby is a memorable character, but his introduction was just stupid. Likewise Gilderoy Lockheart, a character introduced who then disappears without ever influencing the plot at all. Also, this book for me established the notion of Ginny as a primarily annoying character, which made that part of HPB uninteresting.
7: Half-Blood Prince - No Hogwarts feeling whatsoever, but lots of anti-Harry antagonism. I found nothing enjoyable in this book, and many of the characters were unrecognizable as the ones I had got to learn earlier in the series. Especially the one who died - I was just glad to see it happen.