Criminals are most likely transferred to Orlais and Ferelden, conscripted are obviously set free (all those trust issues wouldn't let them keep anyway).
Oh come on now, I would be honourable enough to stick the sword in the front 
I suppose I'd be down with freeing Alexius, but Florianne and Samson?
I um... I had not foreseen this.
That's precisely why my leadership skills are predominant! (Kidding, mostly
)
To make sure there are no err.. loose ends, so to speak. Just kill them. Especially if they deserve it. Some of the prisoners presented didn't.. for instance, when judging that grey warden I sent her to die an honourable death in the deep roads. And I sent the Avvar to Tevinter.. not even sure if the option of killing him was there.
As for Alexius, the Crestwood mayor, Blackwall in some playthroughs.. I had them executed.