Does anyone know of any good run tracking apps that allow for varying run/rest interval periods?

Nike + mapmyride

I use Runkeeper, it's pretty cool. You can set it by miles or time and various intervals. Plus, the app is free.

Garmin has a 220 now that will auto stop if you stop. Map my Run is am app that will pull your pace and display all that stats at the end. You can infer when you are walking etc. Garmin has a coach option that I never use and I believe the app can be preprogrammed as well. I hate the size of the phone and I use my watch. I interval training on a track or the treadmill so it is not something I use the phone for or my watch. Not sure of this helps or not. Let me know if you have more specific questions and will see what I can dig up.

Endomondo is good. I do know it has a "training for" function. i.e.: I want to train for a 5k run in 2 months and I am a couch potato. It will give me a training schedule to get me prepped. First few days may be walk 10 minutes, job 1 minute, etc.

Endomondo basic is free. The interval training is part of the pro (paid for) upgrade.

I even used it with a blue tooth heart monitor to track my effort when in the gym and not moving any distances.

https://www.endomondo.com/

I used the S-Health app on my phone. It starts out very slow then picks up as you maintain a certain pace. These are not like 30 second intervals , it is more like running 3 or 4 minutes at a pace with steady increases in speed. Hope this helps.

Nike + is my favorite, been usinit for about 6-7 years and works great. The new upgrade is a bit strange but I like nonetheless

There was a neat app I used to use called Zombie Run. It kept track of your speed and would tell a small story while you ran. There'd be certain parts where the zombies or bad guys with guns would "chase" you and you'd have to run faster and what not, followed by periods of downtime. Pretty interesting app. Only downside is some of the stories required you to pay for them.