I use My Fitness Pal but I don't like it for a few reason. First, it tells me I should never go below 1200 because doing so puts me in starvation mode (which is absurd because on sedentary days at my height/weight 1000-1100 is necessary to lose), which just annoys me.
Second, I don't really think a lot of the calorie or weight counts are accurate. They are all member-submitted, and even on the ones that have several "confirmations" I've noticed some really incorrect counts on some things. The calculations it gives for the exercises you burn do not factor in height or weight and I mainly just ignore it.
Third, it doesn't count strength training towards your weekly "minutes" of exercise or more importantly towards calories burned. This has on a few occasions led me to skip strength training in exchange for cardio, which is dumb on my part. Of course it is my responsibility to ensure proper health, not my calorie counter, I do wish it gave more proper health support/information by putting more weight on strength training (no pun intended

).
Lastly, I do not like that it keeps macronutrients like protein in the green or "good to go" zone if you don't meet them that day, and red or "warning" zone if you do or go over. Sends the wrong message that eating more protein and fewer grams of fat/carbs one day is a bad thing. Again, my responsibility not my counter's to ensure I'm eating right, but I want my counter to at help in that process, not send the wrong message.