Why did he run? He's a fugitive. What did he do?
Is the Doctor really who we think he is? What do we know of him? As Ian said in An Unearthly Child, 'perhaps if we had a name...'
Do we trust him? Have we been wrong in trusting him all this time? Does it matter?
This is what I think we'll find out in The Name of the Doctor. Not his true name, though [spoiler alert:] River is said to mention it in the finale (Moffat is tricky, though...like he can come up with a Gallifreyan name for our Doctor!) What if we don't like it!!? ;) 'Hello, I'm Ralph. Basically, Run!' But, I think we'll find out who he is, what he's done. Ralph's not a very Gallifreyan name, hmm.
The tagline is 'his greatest secret revealed'. Is his name really his greatest secret, or is it something he did, something terrible?
He's now in trouble, and it seems that Clara is the only one who can save him. In fact, she was born to save him. Maybe all he needs is time. I would love to think of Time being personified, in Clara. I'm not saying that's who she is. I am totally just letting the writer bit of me ... write. I'm letting my imagination get the best of me.