Mine was a tie between Batman by Scott Snyder and The Amazing Spider-Man by Dan Slott. What are yours? Also if you can, include your favorite issue of the year. Mine's either Batman #13 or Amazing Spider-Man #700.
My favorite series has been Geoff John's Aquaman, particularly The Others arc.
As for my favorite issue, Action Comics #9 is one of my favorite issues of all time, despite the atrocious art and Superman not appearing in a single panel. Action Comics #13 has a mediocre main story, but the short back-up feature is the first piece of entertainment to bring a tear to my eye since the ending of Toy Story 3.
I notice alot of people choosing things that only existed for the last few months as their "best of 2012". I looked back at those earlier months trying to find something that had been consistantly good for the entire year. Early 2012 was indeed a bit of a slump, with much of New52 kinda lagging and the first wave of cancelations hitting.
I think for the entire year of 2012, the best run was Avengers Academy. Christos Gage consistantly knocked that one out of the park. Good characters. Good stories. It even survived a crossover with AvX without it starting to stink.