With my new lifestyle (lost 40lbs since January) I have been using my phone as my primary tracking device for all my fitness needs.
Food/Calorie tracking: MyFitnessPal
I love this app. The ability to track everything you eat and all your exercise calories burned is the valuable tool I use. You can make changes on the phone or the website. You can make changes to the items you are tracking on the web site and it really makes the app personalized. For example, I added Pre-Workout and Post Workout meals. I also added Body Fat % to one of the tracked stats.
App Store - Calorie Counter & Diet Tracker by MyFitnessPal
Weight Training Tracking: JeFit Pro
A friend turned me onto Jefit and I love it. It too has a web site interface that lets you build and customize workouts. The DB is huge and there are lots of exercises to choose from when you are building your routines. The workout log and timer are great and help keep you focused in the gym.
App Store - JEFIT PRO Workout
Heart Rate Monitoring: DigiFit app + Wahoo Fitness Blue HR
Monitoring your heart rate is very important, especially for those of us that are getting older. I use this combination to keep track of my heart rate and calories burned. The app is great and has a really nice graphical view of your heart rate zones while you exercise. It works in the background and will use the notification center bars to let you know what zone you are in.
App Store - Digifit?
iPhone 4S heart rate monitor, iPhone 4S heart rate strap, Bluetooth Smart Heart Rate Strap by Wahoo Fitness, Blue HR
Outside Running: RunKeeper (Using it today for the first time )
I have not been able to get in a run outside yet, but I read a lot of reviews and RunKeeper looks like the one to use. I have a few others that I downloaded when the prices went down and will test them all myself, but I am starting with RunKeeper. It also integrates with my Blue HR so I can use just that to track runs outside.
App Store - RunKeeper
I have also used the Couch to 5k app, the 100 pushup app, the 200 situps app, and the 20 chinups app. Those are the apps I used to get myself back into exercise, however I am using the apps listed above now since I am already in a fitness grove.