I always think doing these lists is a bit hard. The reason is that I don't usually get to see the best of a particular year till around March or April of the following year when things get released on DVD. I checked at the numbers website and of the 771 movies released in 2006 I have only seen 70. (That number seems low to me since I rent at least 4-5 a week)

(I am no film critic and you're welcome to make fun of me if you wish.) The movies I enjoyed the most:

Running Scared
Thank You for Smoking
Lonesome Jim
Brick
Lucky Number Slevin
10th & Wolf
World Trade Center
The Descent
Brothers of the Head
Down in the Valley
The King
A Scanner Darkly
Little Miss Sunshine
The Prestige
Babel
The Fountain

Most disappointing (because I was looking forward to something more) or just plain horrible:

The Wicker Man
Freedomland
V for Vendetta
Inside Man
Basic Instinct 2
The Da Vinci Code
Wassup Rockers
The Lady in the Water
The Last Kiss
Miami Vice
Superman Returns
X-men: The Last Stand
The Black Dahlia
Eragon 

Like I said I have seen 5 movies in the theatres in the last 4 months so I think it is safe to say there is a lot missing from both my lists.