Essentially, Jeppesen is an IFR product, Ozrunways is a VFR product. Jepp on the iPad gives commonality / back up with other Jepp products. Its free if you have a Jepp subscription. Ozrunways requires a separate subscription.
The Jepp version of the AIP is searchable and easier to use. ERSA on Ozrunways is better / easier than the airport section of Jepp. I prefer the Jepp chart layout, so it wins there too. In my opinion the Jepp app is more stable. It gets better satellite lock and highlights if it loses satellites. Ozrunways can go into a dead reckoning mode where the aircraft icon continues to move without satellite reception or making it obvious that satellites have been lost. I find Ozrunways to be unreliable in the flight levels (on my old iPad 2, havent yet tried the IPad 3). OzRunways can be confusing about which maps are downloaded to the iPad and which are cloud based. Jepp has everything all the time. I think Jepp is a bit more clear about version status.
They're both good products. If I fly VFR, I use Ozrunways. Navigating the terminal area with the aircraft position on VTC is fantastic. IFR I use Jepp. But IFR, I also have Flitedeck on a Motion CL900 tablet and paper charts as well. In the Sim, I just use Jepp on the iPad.
I use a BT GPS unit with the Motion CL900, but not the iPad. I think a lot of my criticisms of Ozrunways on the iPad disappear with an external GPS. I see that Garmin have just released a bluetooth GPS / Glonass unit aimed at aviation which looks like a good thing.