I use myplate
I like that i can put in my recipes, and also make up meals that i eat regularly (for example my yogurt,granola and fruit is just one button) I love that the food database has everything.
I think most the tools are very similar in all three though.
I know a lot of people really like sparkpeople- I used it for quite a while too and it was nice. They have lots of other resources; recipes, forums, weight training videos, articles, etc.
Fitday was my least favorite. It was harder to navigate, and the database wasn't as extensive as the other two, i had a hard time finding lots of foods that i eat regularly.