I can't choose, so here are my top 4 that spring to mind:
Planetary, just such a great book, it left me wanting more though.
DC: The New Frontier, I loved this whole book, especially how they made Martian Manhunter interesting on his own for once. Not only that. but it also has one of the most heartbreaking side stories I've ever read, John Henry. Just John Henry.
The Astounding Wolf-Man was amazing, a really great synthesis of monster and superhero mythology, plus, watching a man's life crash and burn is always a blast. It really left me wishing it wouldn't end.
The Age of the Sentry, a really short and sweet miniseries and a fun melding of the differing Marvel and DC Silver Age styles.