- They are both well backed (Heroku by Salesforce money/profits, Parse by great investors), have awesome founders, talented employees, and are both YC companies.
- Parse is pretty much 100% mobile focused. This is their bread and butter.
- Heroku is Polyglot and spans dozens of platforms on multiple OS's, with no real focus.
I think this comes down to where you run the rest of your stack, how tightly you want things integrated, and which service is the easiest to use and most reliable. Is mobile 99% of what you do? Parse is probably the best choice. Is mobile 25% of your business and you're already using Heroku for everything else? I could go either way here. We use Heroku and AWS to drive 100% of our platform, but we're also not mobile (yet). I personally know the Parse guys and they are outstanding at what they do and growing at a phenomenal rate, so when we do dive into mobile I'll likely be giving them a shot first.