I used an excel spreadsheet for a long time - it worked just fine. I now use Fitday - I like being able to create reports and see my ratios of percentage of calories from fat/protein/carbs.
Like Kate said - find what works for you.
I think logging and planning ahead have been key for me. When I stop logging is when the weight starts to creep up...
I
calorie king dot com and thedailyplate dot com for looking things up that aren't in Fitday. Also really good for checking out what might be a good choice if you are going to a chain restaurant.