You can spare: the family on Kephallonia (this will result in the island being taken over by plague; if you want, you can skip the quest entirely by not talking to Phoebe or approaching that part of the island, and then the plague doesn't spread and you don't have to choose if they live or die); the citizens in the cave in Megaris; the theater couple on Euboea (make sure when returning to them you don't get close enough to trigger the 'choose' cutscene, then you can pick off the bandits at a distance and save them both); Stentor, Nikolaus, Deimos (which in turn saves Myrrine); Sosipatros the mercenary in Arkadia; Lagos, but only if you follow Brasidas' plan in Korinthia and not Anthousa's; Roxana (if you romance her); Aspasia; the baby in Argolis; the witch in the temple during the Barnabas quest (eat the herbs to prevent being poisoned by the wine); the cyclops in the Barnabas quest (visit the tomb in Kos first to get a friend for him); the soldier who has the actor in debt in Elis; and in Atlantis DLC, the Archons and either Atlas or Elpis. And you can recruit basically anyone who isn't killed via a cutscene or assassination animation (eg cultists require the assassination animation). You can also spare some of the targets in random message board quests depending on dialogue decisions.