1. Assassins Creed II - In my opinion this is still the best AC has to offer. Apart from introducing one of the better protagonists (Not Desmond) in gaming it's tale of revenge and intrigue is easily the most powerful of the series.
2. Assassins Creed IV: Black Flag - I'm not that far into it but I can already tell this is a return to what I liked about the series initially. Much like Enzio, Edward is his own breed of Assassin and manages to be memorable even with a more action based premise. The story has become so convoluted over the years it's overshadowed the unique world and intricate detail that goes into each title. Black Flag is a return to form.
3. Assassins Creed: Brotherhood - While it has a expansion feel, it improves on 2 in several ways. Most notably the introduction of recruiting and utilization of your own squad of assassins.
4. Assassins Creed III - This game is a mixed bowl to say the least. The world it presents is perhaps the most interesting in the series. American Revolution experienced through the eyes of a native American badass? This should be a home run of epic proportions. Unfortunately the story, protagonist (Seriously Connor and his Dad are bland as ****) and overall pacing are by far the weakest AC has to offer.
5. Assassins Creed Revelations - I felt this game offered nothing new to the Enzio trilogy and thusly deserves to be the bottom of the barrel.
Edit: I have only played the first Assassins Creed for 20 minutes so to be fair I have not included it in this list.