My favorite is RunKeeper, which I use to track my fitness routines. It does more than track runs – I use it to track my bike rides as well as to log my strength training workouts through one of the add-on “apps” (I use StrongerApp).
My second favorite is LoseIt!, which I use to track caloric budget. With it, I’ve lost 20 pounds over the last 9 months.
Both of these apps have a prominent place on my iPhone’s first app page.