There are two online programs that I have used to count calories and both have fantastic apps for your phone as well. It is quicker to enter everything in on the desktop, but having the phone to search when you are out at a restaurant can be key to choosing a healthy entree.
My Fitness Pal is great because it is quick to use on the phone, and has a great community where you can make friends to support you. They have updates similar to Facebook that show your exercise and weight loss progress. I like to see what other people are doing for exercise, and it pushes me to work out longer and harder if I see someone else on a roll.
Fat Secret also have a great community, but I found it took me longer to enter my foods into their online application. The best thing about Fat Secret is if you use their Diet Calendar feature you can see how many calories you have burned through day to day activities and exercise vs how many calories you ate. This helps me to keep on track and maintain your weight, and could also be used as a tool for weight loss. Currently I try to eat a few hundred calories below what I am burning so I am not starving myself, and I have been maintaining my weight for over a year now with this method.