My favorite book of the series would easily be Eclipse; it had the most action in it as far as a large battle, the death of Victoria. The mystery of who was in Bella's room. The love that Jacob had for Bella intensifying beside Bella/Edwards relationship changing into a more grown up, in depth relationship other than Bella being dazzled and Edward being overprotective and brooding.
Also, it has some of the best parts in the entire series - The story of Jasper. The story of Rosalie. The Quileute (pretty sure I misspelled that) Legends. You know the pack better and you really start to feel for Jacob's torture in this book and start to feel sorry for him. In New Moon he just seemed like a love sick teenager, but in Eclipse you can tell how deeply he was hurt.
Anyway, Eclipse is my favorite, Breaking Dawn my least.