Nuncio and Zevran
If Zevran died in Origins, Nuncio won't appear. If he's alive, you'll be asked by this supposed Antivan lawmaker to track down a dangerous murderer - who turns out, surprise surprise, to be Zevran. Nuncio is actually a Crow on the hunt for the reformed assassin. You can then either hand Zevran back over to Nuncio (you dick!) or let him go, in which case he helps out against his former employers and shows up for the final battle.
Given that Zevran makes a convincing claim for Nuncio having lied, it's hard to figure out exactly who would still hand him over for the reward - but then again, there are people to hand Isabella over to the Arishok.
If Nathaniel survived the events of Awakening then you'll be asked, in Act 3, to rescue him from the Deep Roads. His death is presumed to occur if Hawke ignores the quest, whereas saving him is guaranteed if you take it on. If saved, Nathaniel shows up for the final battle.
Gamlen and Charade
Easy to miss, this. Finding a note on Gamlen's desk in his home in Lowtown leads to a lengthy treasure hunt that ends with the discovery of Gamlen's long-lost daughter, Charade. At the end Hawke can either decide to return the gem to his uncle or reunite him with his daughter - it's a choice between gold and family.
Discovering a conspiracy against the increasingly tyrannical Knight Commander, it's up to Hawke to choose whether or not to take this information to Meredith directly or allow the First Enchanter, Orsino, to deal with it quietly. A pro-Templar Hawke would prefer the former, a mage the latter.
Keran, Act 3
Keran shows up again as part of the conspiracy in Act 3. Hawke can have him killed for his involvement, which threatened the life of one of Hawke's siblings (or Fenris, if both are dead). Alternatively he can be freed by a clement Hawke, or handed back to the Templars if you see that as the best way to bring him in line. This is a choice between vegeance, mercy and authority.
Of all of the apostates that Meredith asks you to track down, Emile is the only harmless one. He's lying about being a blood mage to pick up girls in the tavern, and begs you to let him go so that he can experience life outside of the circle - a request that an apostate Hawke may be sympathetic to. On the other hand, he's an idiot and the Circle is probably the best way to protect him from himself.
The dragon in the Bone Pit
Your final trip to the Bone Pit does actually involve a dragon. This is a straight-up boss fight that you either did or didn't do. Doing it, however, grants Hawke the Armor of the Champion - what you'll see him or her wearing whenever they're depicted elsewhere.
The mages and the Templars
It all comes down to this: when Anders destroyed the Chantry and Meredith invoked the Rite of Annulment, whose side did Hawke take? This decision has the potential to split the party if you've not paid attention to your companions, and is the single biggest factor in the way that Hawke is remembered after the events of the game - including determining his or her reputation in Inquisition. By now, you should know which way your Hawke has been leaning. Time to make a final call.
While Mark of the Assassin only has a cursory relationship with Inquisition, Legacy is much more relevant - to the extent that I'd recommend you go back and play it if you haven't already. There are two choices to make here.
'Malcolm's will' is straightforward - you either helped Hawke discover records left by his mage father or you didn't. The other decision, however, is a big one.
Hawke discovers an ancient, intelligent darkspawn in an Warden prison. This darkspawn - Corypheus - has been manipulating Wardens through the darkspawn taint. A Blighted former Warden commander with a shady history, Larius, implores you to free Corypheus and kill him once and for all. The current Warden commander, Janeka, wishes to free Corypheus and use the creature to find a solution to the Blight - a similar attitude to that of the Warden Commander in Awakening if you chose to spare the Architect. It's heavily implied that Janeka is under Corpheus' influence.
Siding with Larius means ignoring the fact that he blackmailed Hawke's father into imprisoning Corypheus in the first place. Siding with Janeka means taking the risk that Corypheus wants you to free and imprison him. Make your choice.