OK, so I'm sure there are hundreds out there that I haven't even begun to explore, but these are my favourites.
Honourable Mention goes to My Fitness Pal, I don't use it for anything related to exercise but it is a useful way to check or keep track of calories consumed on the run (not literally :P) I love the 12WBT meal plans because I don't really need to do that unless I'm eating out - I know I have my three meals taken care of, and as long I stick to two 150-cal snacks, or three 100-cal snacks, I know I'm fine with my calories for the day.
Fourth place goes to Couch to 5k. This is the app that originally got me running last autumn before I slacked off over winter. It is great for beginner runners, and completely idiot-proof. You can set your own playlist, pause, see how long you have left. It's interval training simplified because it tells you when to walk and when to run. I will add that when I 'graduated' the program I was not running 5km, for a beginner female runner 5km in 30 minutes would be a pretty good pace. But that's not really important; I was running for 30 minutes straight and from there it's quite simple to build distance. There's also a Bridge to 10km app to go from 5 to 10, but I just did it on my own.
Third place goes to 100 Pushups, of which there are many out there essentially the same. Like C25k, you gradually build up your push-up reps with the idea you'll be doing 100 by the end. I'll update you on my progress at the end of the round. Again - simple but effective, takes the thought out of the exercise. JFDI!
Second place goes to an old fave, RunKeeper. It tracks how far I've run, it tracks my pace, I can link it in to the website to graph my progress over time. I pick which playlist I want, there are coaching options, the list goes on! Downside is the GPS often plays up around water or under lots of trees, but overall, it's brilliant. I can post straight to Facebook and show off my long runs too.
And my brand new favourite is the Nike Training Club app. If you, like me, need to work out at home sometimes, but just can't get into DVDs or want a change, this is a brilliant app. Even Michelle Bridges's DVDs, I just don't enjoy that much. With the NTC workouts, there is so much choice. You can choose the focus of your workout, the length, the fitness level. And then I can pop on the TV or some music while I do it. It also has video instructions for all the exercises if you need them, and requires minimal equipment. Absolutely love it and it's going to make my life easier this round!