I love MyNetDiary. Most of the foods I eat are in there and if I can't find it, there are some I can scan the barcode with my phone and it will put in the nutritional information. It has a place for me to count my glasses of water (you touch each glass as you drink it), it tells me at the end of the day how I'm doing with my sodium, fiber, saturated fat, etc. It keeps track of what I should be consuming, calorie-wise and deducts the calories I'm consuming so I know where I'm at during the day with my eating. There is a place for my exercise and when it's completed, it will count that in towards my calorie-count for the day. I can enter my measurements in there as I take them and there is even a section for vitamins/meds (I haven't used that section yet).
I also like Workout Trainer for quick ideas for exercises. I haven't used it much but so far, I like it.