I've long been an advocate of counting calories to lose weight and have lost the most weight over the years by keeping a journal and writing down everything that passes my lips.
Hop on over to Shawn Tyler Weeks' blog to see how he lost over 200 pounds by counting calories here.
He recommends My Fitness Pal to calculate calories burned.
One of the books I like to use to calculate calories in food is the Calorie King book. Another great site is Dottie's Weight Loss Zone. This is especially good for calculating calories in restaurant meals.