I have used both and both have been very good tools, depending on my diet at the time. Caloriecount.com keeps track of a lot more things, including vitamin levels, but doesn't have too extensive a database for certain foods and exercise. Keep in mind that it being caloriecount, it tracks calories, so if you're on a carb-counting diet, this may not be for you.

I'm currently using loseit.com because the app is so much easier to use and a lot more user-friendly. The database for food seems a lot more extensive and accurate, though it doesn't seem to monitor water intake or vitamin intake at all. The emphasis for this site seems to be a calorie counter as well.